[Freesurfer] Monte Carlo for lme

[Knut J Bjuland]

External Email - Use Caution

Dear Freesurfer experts,




I am looking into Monte Carlo simulation to control for multiple comparisons 
for lme in Matlab. Are there any good library that has implemented this in 
Matlab?



Best regards




Knut Jørgen Bjuland PhD





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Re: [Freesurfer] Monte Carlo threshold p-values

[Douglas N. Greve]

1.3 is not a z value, it is -log10(.05)

On 07/06/2018 10:15 AM, Dincer, Aylin wrote:
>
>
> Hello FreeSurfer experts,
>
>
> In the FreeSurfer wiki page regarding multiple comparisons 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
> ) under "Simulation", it mentions the common Monte Carlo thresholds 
> and their associated p-values.  Would you be able to explain how 
> the associated p values for each z threshold was calculated? (Ex. The 
> associated p-value for z=1.3 is 0.05)
>
>
> Thank you!
>
> Aylin
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on 
> the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
>
>
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Re: [Freesurfer] Monte Carlo simulation - vertex wise threshold question

[Douglas N. Greve]

Yes, 3 is p<.001, which is converted to a z before thresholding the map. 
Note that we are trying to push people to use permutation instead of MC.

On 07/09/2018 05:22 PM, Dincer, Aylin wrote:
>
>
> Hi FreeSurfer experts,
>
>
> I am trying to understand the Monte Carlo Z simulation in FreeSufer 
> (/mri_glmfit/-/sim/) and have a question about the vertex wise 
> /cluster forming threshold.
>
>
> In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set 
> and the threshold is applied to a z map. Is the 3 threshold (p value 
> of 0.001) converted to a z score using the z table before it is 
> applied to the map?
>
>
> Thanks!
>
> Aylin
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on 
> the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
>
>
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[Freesurfer] Monte Carlo simulation - vertex wise threshold question

[Dincer, Aylin]

External Email - Use Caution

Hi FreeSurfer experts,


I am trying to understand the Monte Carlo Z simulation in FreeSufer 
(mri_glmfit-sim) and have a question about the vertex wise /cluster forming 
threshold.


In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set and the 
threshold is applied to a z map. Is the 3 threshold (p value of 0.001) 
converted to a z score using the z table before it is applied to the map?


Thanks!

Aylin


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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[Freesurfer] Monte Carlo threshold p-values

[Dincer, Aylin]

External Email - Use Caution

Hello FreeSurfer experts,


In the FreeSurfer wiki page regarding multiple comparisons 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
) under "Simulation", it mentions the common Monte Carlo thresholds and their 
associated p-values.  Would you be able to explain how the associated p values 
for each z threshold was calculated? (Ex. The associated p-value for z=1.3 is 
0.05)


Thank you!

Aylin


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas N Greve]

I don't know, you'll have to look at how you computed the first frame. 
Maybe the 1st and 2nd time point for that subject are the same


On 02/05/2018 04:27 PM, miracle ozzoude wrote:
> Hello Doug,
>
> Thank you. How do i got about fixing? Do you think it's a good idea to 
> start afresh on this subject (i.e. recon-all and longitudinal pipeline)?
>
> Best,
> Paul
>
> On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve 
> > wrote:
>
> The first frame in your input file is all 0s, so something is
> wrong with the fist subject
>
>
> On 2/3/18 3:03 PM, miracle ozzoude wrote:
>> Hello Doug,
>>
>> I have uploaded the files you requested. Thank you for your help.
>>
>> Best,
>> Paul
>>
>> On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve
>> > wrote:
>>
>> Can you upload the glmfit folders and the glmfit input (--y
>> file) to our filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>> 
>>
>>
>> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>>> Hello Doug,
>>>
>>> I have attached a screen shot of the mask.mgh for both right
>>> and left hemispheres. Everything looks yellow. I followed
>>> the paired t-test tutorial on the wiki page (included my
>>> scripts, fsgd files, and matrix in email thread). How do i
>>> go about fixing it? Thanks you
>>>
>>> Best,
>>> Paul
>>>
>>> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve
>>> >> > wrote:
>>>
>>> that usually means that something has gone wrong with
>>> the analysis. Do the maps look ok? In particular, look
>>> at the mask
>>>
>>>
>>>
>>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
 Hello Doug,

 I tried using the MC tables that FS distributed.
 However, i got an error about " cannot find
 /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
 fwhm00, the table starts from fwhm01 to fwhm30. Below
 are my script and cache.mri_glmfi-sim.log files. My
 FreeSurfer version is stable version 5.3 on mac. Thank
 you.

 Best,
 Paul

 mri_glmfit-sim --glmdir lh.paired.diff.glmdir
 --cache-dir
 $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex
 --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
 mri_glmfit-sim --glmdir rh.paired.diff.glmdir
 --cache-dir
 $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex
 --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite

 On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
 > wrote:

 Why are you doing your own MC simulation? You can
 just use the tables that we distribute ...


 On 1/17/18 6:12 PM, miracle ozzoude wrote:
> Hello Experts,
>
> I am running a paired t-test cortical thickness
> analysis based on the instruction on the wiki page
> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> 
> ).
> However, the monte carlo files weren't not created
> when i corrected for multiple comparisons. Below
> are my script, fsgd files, mc-z log file, and a
> screenshot of contrast folder missing mc.z maps.
> Please can you help me figure out why the error is
> happening. Thank you.
>
> Best,
> Paul
>
> *Script*:
> pairs=pairs.fsgd paired=paired_diff.fsgd
> martrix1=mean.mtx martrix2=age.mtx
> #resample each subjects's left and right
> hemisphere data to fsavarage.
> mris_preproc --target fsaverage --hemi lh --meas
> thickness --out lh.paired-diff.thickness.mgh
> --fsgd $pairs --paired-diff
> mris_preproc --target fsaverage --hemi rh --meas
> thickness --out rh.paired-diff.thickness.mgh
> --fsgd $pairs --paired-diff
> # #smoothen the concatenated file by 5mm FWHM.
> --cortex means only smooth areas in the cortex.
> N:B. 

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

Thank you. How do i got about fixing? Do you think it's a good idea to
start afresh on this subject (i.e. recon-all and longitudinal pipeline)?

Best,
Paul

On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve 
wrote:

> The first frame in your input file is all 0s, so something is wrong with
> the fist subject
>
> On 2/3/18 3:03 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have uploaded the files you requested. Thank you for your help.
>
> Best,
> Paul
>
> On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
> wrote:
>
>> Can you upload the glmfit folders and the glmfit input (--y file) to our
>> filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>
>> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>>
>> Hello Doug,
>>
>> I have attached a screen shot of the mask.mgh for both right and left
>> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
>> on the wiki page (included my scripts, fsgd files, and matrix in email
>> thread). How do i go about fixing it? Thanks you
>>
>> Best,
>> Paul
>>
>> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve > > wrote:
>>
>>> that usually means that something has gone wrong with the analysis. Do
>>> the maps look ok? In particular, look at the mask
>>>
>>>
>>>
>>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
>>>
>>> Hello Doug,
>>>
>>> I tried using the MC tables that FS distributed. However, i got an error
>>> about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
>>> fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
>>> cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
>>> on mac. Thank you.
>>>
>>> Best,
>>> Paul
>>>
>>> mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
>>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
>>> --cwpvalthresh 0.05 --2spaces --overwrite
>>> mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
>>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
>>> --cwpvalthresh 0.05 --2spaces --overwrite
>>>
>>> On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
 Why are you doing your own MC simulation? You can just use the tables
 that we distribute ...

 On 1/17/18 6:12 PM, miracle ozzoude wrote:

 Hello Experts,

 I am running a paired t-test cortical thickness analysis based on the
 instruction on the wiki page (https://surfer.nmr.mgh.harvar
 d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't
 not created when i corrected for multiple comparisons. Below are my script,
 fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
 maps. Please can you help me figure out why the error is happening. Thank
 you.

 Best,
 Paul

 *Script*:
 pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
 martrix2=age.mtx
 #resample each subjects's left and right hemisphere data to fsavarage.
 mris_preproc --target fsaverage --hemi lh --meas thickness --out
 lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
 mris_preproc --target fsaverage --hemi rh --meas thickness --out
 rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
 # #smoothen the concatenated file by 5mm FWHM. --cortex means only
 smooth areas in the cortex. N:B. FWHM changes based on study type.
 mri_surf2surf --hemi lh --s fsaverage --sval
 lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
 lh.paired-diff.thickness.sm05.mgh
 mri_surf2surf --hemi rh --s fsaverage --sval
 rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
 rh.paired-diff.thickness.sm05.mgh
 # #Run GLM analysis
 mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
 $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
 lh.paired-diff.glmdirir
 mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
 $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
 rh.paired-diff.glmdir
 # # #Run Clusterwise correction for multiple comparisons using MONTE
 CARLO. First create a table for of simulations
 mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
 mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
 *Fsgd file 1:pairs.fsgd*

 GroupDescriptorFile 1

 Class ADEX

 Input 1000_1 ADEX

 Input 1000_2 ADEX

 Input 1001_1 ADEX

 Input 1001_2 ADEX

 Input 1003_1 ADEX

 Input 1003_2 ADEX

 Input 1005_1 ADEX

 Input 1005_2 ADEX

 Input 1008_1 ADEX

 Input 1008_2 ADEX

 Input 1013_1 ADEX

 Input 1013_2 ADEX

 Input 1014_1 

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

The first frame in your input file is all 0s, so something is wrong with 
the fist subject



On 2/3/18 3:03 PM, miracle ozzoude wrote:

Hello Doug,

I have uploaded the files you requested. Thank you for your help.

Best,
Paul

On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
> wrote:


Can you upload the glmfit folders and the glmfit input (--y file)
to our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2/



On 2/1/18 7:46 PM, miracle ozzoude wrote:

Hello Doug,

I have attached a screen shot of the mask.mgh for both right and
left hemispheres. Everything looks yellow. I followed the paired
t-test tutorial on the wiki page (included my scripts, fsgd
files, and matrix in email thread). How do i go about fixing it?
Thanks you

Best,
Paul

On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve
> wrote:

that usually means that something has gone wrong with the
analysis. Do the maps look ok? In particular, look at the mask



On 1/20/18 1:56 PM, miracle ozzoude wrote:

Hello Doug,

I tried using the MC tables that FS distributed. However, i
got an error about " cannot find /fwhm00/pos/th30/mc-z.csd
". I checked and there's no fwhm00, the table starts from
fwhm01 to fwhm30. Below are my script and
cache.mri_glmfi-sim.log files. My FreeSurfer version is
stable version 5.3 on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex
--cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex
--cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite

On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
> wrote:

Why are you doing your own MC simulation? You can just
use the tables that we distribute ...


On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness
analysis based on the instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
).
However, the monte carlo files weren't not created when
i corrected for multiple comparisons. Below are my
script, fsgd files, mc-z log file, and a screenshot of
contrast folder missing mc.z maps. Please can you help
me figure out why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd
martrix1=mean.mtx martrix2=age.mtx
#resample each subjects's left and right hemisphere
data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas
thickness --out lh.paired-diff.thickness.mgh --fsgd
$pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas
thickness --out rh.paired-diff.thickness.mgh --fsgd
$pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex
means only smooth areas in the cortex. N:B. FWHM
changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage lh
--cortex --glmdir lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage rh
--cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple
comparisons using MONTE CARLO. First create a table for
of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim
mc-z 1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh
0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim
mc-z 1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh
0.05 --2spaces --overwrite
*Fsgd file 1:pairs.fsgd*

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

I have uploaded the files you requested. Thank you for your help.

Best,
Paul

On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
wrote:

> Can you upload the glmfit folders and the glmfit input (--y file) to our
> filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have attached a screen shot of the mask.mgh for both right and left
> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
> on the wiki page (included my scripts, fsgd files, and matrix in email
> thread). How do i go about fixing it? Thanks you
>
> Best,
> Paul
>
> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve 
> wrote:
>
>> that usually means that something has gone wrong with the analysis. Do
>> the maps look ok? In particular, look at the mask
>>
>>
>>
>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
>>
>> Hello Doug,
>>
>> I tried using the MC tables that FS distributed. However, i got an error
>> about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
>> fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
>> cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
>> on mac. Thank you.
>>
>> Best,
>> Paul
>>
>> mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
>> --cwpvalthresh 0.05 --2spaces --overwrite
>> mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
>> --cwpvalthresh 0.05 --2spaces --overwrite
>>
>> On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve > > wrote:
>>
>>> Why are you doing your own MC simulation? You can just use the tables
>>> that we distribute ...
>>>
>>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>>>
>>> Hello Experts,
>>>
>>> I am running a paired t-test cortical thickness analysis based on the
>>> instruction on the wiki page (https://surfer.nmr.mgh.harvar
>>> d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't
>>> not created when i corrected for multiple comparisons. Below are my script,
>>> fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
>>> maps. Please can you help me figure out why the error is happening. Thank
>>> you.
>>>
>>> Best,
>>> Paul
>>>
>>> *Script*:
>>> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
>>> martrix2=age.mtx
>>> #resample each subjects's left and right hemisphere data to fsavarage.
>>> mris_preproc --target fsaverage --hemi lh --meas thickness --out
>>> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>> mris_preproc --target fsaverage --hemi rh --meas thickness --out
>>> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>> # #smoothen the concatenated file by 5mm FWHM. --cortex means only
>>> smooth areas in the cortex. N:B. FWHM changes based on study type.
>>> mri_surf2surf --hemi lh --s fsaverage --sval
>>> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>> lh.paired-diff.thickness.sm05.mgh
>>> mri_surf2surf --hemi rh --s fsaverage --sval
>>> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>> rh.paired-diff.thickness.sm05.mgh
>>> # #Run GLM analysis
>>> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
>>> lh.paired-diff.glmdirir
>>> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
>>> rh.paired-diff.glmdir
>>> # # #Run Clusterwise correction for multiple comparisons using MONTE
>>> CARLO. First create a table for of simulations
>>> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
>>> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>>> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
>>> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>>> *Fsgd file 1:pairs.fsgd*
>>>
>>> GroupDescriptorFile 1
>>>
>>> Class ADEX
>>>
>>> Input 1000_1 ADEX
>>>
>>> Input 1000_2 ADEX
>>>
>>> Input 1001_1 ADEX
>>>
>>> Input 1001_2 ADEX
>>>
>>> Input 1003_1 ADEX
>>>
>>> Input 1003_2 ADEX
>>>
>>> Input 1005_1 ADEX
>>>
>>> Input 1005_2 ADEX
>>>
>>> Input 1008_1 ADEX
>>>
>>> Input 1008_2 ADEX
>>>
>>> Input 1013_1 ADEX
>>>
>>> Input 1013_2 ADEX
>>>
>>> Input 1014_1 ADEX
>>>
>>> Input 1014_2 ADEX
>>> *Fsgd file 2: paired_diff.fsgd*
>>>
>>> GroupDescriptorFile 1
>>>
>>> Class ADEX
>>>
>>> Variables Age
>>>
>>> Input 1000 ADEX 72
>>>
>>> Input 1001 ADEX 76
>>>
>>> Input 1003 ADEX 72
>>>
>>> Input 1005 ADEX 80
>>>
>>> Input 1008 ADEX 72
>>>
>>> Input 1013 ADEX 80
>>>
>>> Input 1014 ADEX 80
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> 

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

Can you upload the glmfit folders and the glmfit input (--y file) to our 
filedrop?


https://gate.nmr.mgh.harvard.edu/filedrop2/


On 2/1/18 7:46 PM, miracle ozzoude wrote:

Hello Doug,

I have attached a screen shot of the mask.mgh for both right and left 
hemispheres. Everything looks yellow. I followed the paired t-test 
tutorial on the wiki page (included my scripts, fsgd files, and matrix 
in email thread). How do i go about fixing it? Thanks you


Best,
Paul

On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve 
> wrote:


that usually means that something has gone wrong with the
analysis. Do the maps look ok? In particular, look at the mask



On 1/20/18 1:56 PM, miracle ozzoude wrote:

Hello Doug,

I tried using the MC tables that FS distributed. However, i got
an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I
checked and there's no fwhm00, the table starts from fwhm01 to
fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My
FreeSurfer version is stable version 5.3 on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3
pos --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3
pos --cwpvalthresh 0.05 --2spaces --overwrite

On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
> wrote:

Why are you doing your own MC simulation? You can just use
the tables that we distribute ...


On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness analysis
based on the instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
).
However, the monte carlo files weren't not created when i
corrected for multiple comparisons. Below are my script,
fsgd files, mc-z log file, and a screenshot of contrast
folder missing mc.z maps. Please can you help me figure out
why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
martrix2=age.mtx
#resample each subjects's left and right hemisphere data to
fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness
--out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness
--out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex
means only smooth areas in the cortex. N:B. FWHM changes
based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage lh
--cortex --glmdir lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage rh
--cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons
using MONTE CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z
1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05
--2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z
1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05
--2spaces --overwrite
*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

that usually means that something has gone wrong with the analysis. Do 
the maps look ok? In particular, look at the mask




On 1/20/18 1:56 PM, miracle ozzoude wrote:

Hello Doug,

I tried using the MC tables that FS distributed. However, i got an 
error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and 
there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are 
my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is 
stable version 5.3 on mac. Thank you.


Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir 
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos 
--cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir 
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos 
--cwpvalthresh 0.05 --2spaces --overwrite


On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve 
> wrote:


Why are you doing your own MC simulation? You can just use the
tables that we distribute ...


On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness analysis based on
the instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
).
However, the monte carlo files weren't not created when i
corrected for multiple comparisons. Below are my script, fsgd
files, mc-z log file, and a screenshot of contrast folder missing
mc.z maps. Please can you help me figure out why the error is
happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
martrix2=age.mtx
#resample each subjects's left and right hemisphere data to
fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means
only smooth areas in the cortex. N:B. FWHM changes based on study
type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired
--C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired
--C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using
MONTE CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80



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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

I tried using the MC tables that FS distributed. However, i got an error
about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite



On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve 
wrote:

> Why are you doing your own MC simulation? You can just use the tables that
> we distribute ...
>
> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>
> Hello Experts,
>
> I am running a paired t-test cortical thickness analysis based on the
> instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/
> PairedAnalysis). However, the monte carlo files weren't not created when
> i corrected for multiple comparisons. Below are my script, fsgd files, mc-z
> log file, and a screenshot of contrast folder missing mc.z maps. Please can
> you help me figure out why the error is happening. Thank you.
>
> Best,
> Paul
>
> *Script*:
> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx
> #resample each subjects's left and right hemisphere data to fsavarage.
> mris_preproc --target fsaverage --hemi lh --meas thickness --out
> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> mris_preproc --target fsaverage --hemi rh --meas thickness --out
> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth
> areas in the cortex. N:B. FWHM changes based on study type.
> mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh
> --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
> mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh
> --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
> # #Run GLM analysis
> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
> lh.paired-diff.glmdirir
> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
> rh.paired-diff.glmdir
> # # #Run Clusterwise correction for multiple comparisons using MONTE
> CARLO. First create a table for of simulations
> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> *Fsgd file 1:pairs.fsgd*
>
> GroupDescriptorFile 1
>
> Class ADEX
>
> Input 1000_1 ADEX
>
> Input 1000_2 ADEX
>
> Input 1001_1 ADEX
>
> Input 1001_2 ADEX
>
> Input 1003_1 ADEX
>
> Input 1003_2 ADEX
>
> Input 1005_1 ADEX
>
> Input 1005_2 ADEX
>
> Input 1008_1 ADEX
>
> Input 1008_2 ADEX
>
> Input 1013_1 ADEX
>
> Input 1013_2 ADEX
>
> Input 1014_1 ADEX
>
> Input 1014_2 ADEX
> *Fsgd file 2: paired_diff.fsgd*
>
> GroupDescriptorFile 1
>
> Class ADEX
>
> Variables Age
>
> Input 1000 ADEX 72
>
> Input 1001 ADEX 76
>
> Input 1003 ADEX 72
>
> Input 1005 ADEX 80
>
> Input 1008 ADEX 72
>
> Input 1013 ADEX 80
>
> Input 1014 ADEX 80
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


cache.mri_glmfit-sim.log
Description: Binary data
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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug, 
Thanks for responding. I am running a whole brain analysis as result shouldn’t 
I build my own MC simulation? 
Best, 
Paul 

Sent from my iPhone

> On Jan 18, 2018, at 5:23 PM, Douglas Greve  wrote:
> 
> Why are you doing your own MC simulation? You can just use the tables that we 
> distribute ...
> 
>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>> Hello Experts, 
>> 
>> I am running a paired t-test cortical thickness analysis based on the 
>> instruction on the wiki page 
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the 
>> monte carlo files weren't not created when i corrected for multiple 
>> comparisons. Below are my script, fsgd files, mc-z log file, and a 
>> screenshot of contrast folder missing mc.z maps. Please can you help me 
>> figure out why the error is happening. Thank you.
>> 
>> Best, 
>> Paul
>> 
>> Script: 
>> pairs=pairs.fsgd
>> paired=paired_diff.fsgd
>> martrix1=mean.mtx
>> martrix2=age.mtx
>> 
>> #resample each subjects's left and right hemisphere data to fsavarage. 
>> mris_preproc --target fsaverage --hemi lh --meas thickness --out 
>> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>> mris_preproc --target fsaverage --hemi rh --meas thickness --out 
>> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>> 
>> 
>> # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth 
>> areas in the cortex. N:B. FWHM changes based on study type.
>> mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh 
>> --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
>> mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh 
>> --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
>> 
>> # #Run GLM analysis
>> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C 
>> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir 
>> lh.paired-diff.glmdirir
>> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C 
>> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir 
>> rh.paired-diff.glmdir
>> 
>> # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. 
>> First create a table for of simulations 
>> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2 
>> --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2 
>> --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>> 
>> Fsgd file 1:pairs.fsgd
>> GroupDescriptorFile 1
>> 
>> Class ADEX
>> 
>> Input 1000_1 ADEX
>> 
>> Input 1000_2 ADEX
>> 
>> Input 1001_1 ADEX
>> 
>> Input 1001_2 ADEX
>> 
>> Input 1003_1 ADEX
>> 
>> Input 1003_2 ADEX
>> 
>> Input 1005_1 ADEX
>> 
>> Input 1005_2 ADEX
>> 
>> Input 1008_1 ADEX
>> 
>> Input 1008_2 ADEX
>> 
>> Input 1013_1 ADEX
>> 
>> Input 1013_2 ADEX
>> 
>> Input 1014_1 ADEX
>> 
>> Input 1014_2 ADEX
>> 
>> Fsgd file 2: paired_diff.fsgd
>> 
>> GroupDescriptorFile 1
>> 
>> Class ADEX
>> 
>> Variables Age
>> 
>> Input 1000 ADEX 72
>> 
>> Input 1001 ADEX 76
>> 
>> Input 1003 ADEX 72
>> 
>> Input 1005 ADEX 80
>> 
>> Input 1008 ADEX 72
>> 
>> Input 1013 ADEX 80
>> 
>> Input 1014 ADEX 80
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

Why are you doing your own MC simulation? You can just use the tables 
that we distribute ...



On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness analysis based on the 
instruction on the wiki page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, 
the monte carlo files weren't not created when i corrected for 
multiple comparisons. Below are my script, fsgd files, mc-z log file, 
and a screenshot of contrast folder missing mc.z maps. Please can you 
help me figure out why the error is happening. Thank you.


Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx 
martrix2=age.mtx

#resample each subjects's left and right hemisphere data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out 
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out 
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means only 
smooth areas in the cortex. N:B. FWHM changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval 
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval 
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval 
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval 
rh.paired-diff.thickness.sm05.mgh

# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C 
$martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir 
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C 
$martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir 
rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using MONTE 
CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2 
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2 
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite

*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80



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[Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Experts,

I am running a paired t-test cortical thickness analysis based on the
instruction on the wiki page (
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the
monte carlo files weren't not created when i corrected for multiple
comparisons. Below are my script, fsgd files, mc-z log file, and a
screenshot of contrast folder missing mc.z maps. Please can you help me
figure out why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx

#resample each subjects's left and right hemisphere data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff


# #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth
areas in the cortex. N:B. FWHM changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh
--fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh
--fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh

# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
rh.paired-diff.glmdir

# # #Run Clusterwise correction for multiple comparisons using MONTE CARLO.
First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2
--sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2
--sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite

*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80


mc-z.abs.2.mri_glmfit-sim.log
Description: Binary data
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Re: [Freesurfer] Monte-Carlo f-test

[Douglas Greve]

In theory it is because the F can be converted to a p which can be 
converted into a pseudo-z. When you run mri_glmfit-sim, you should make 
sure to use an unsigned test ("abs")



On 12/22/17 8:08 PM, basile pinsard wrote:

Hi Freesurfer experts.
Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable 
for F-test?
The doc says that it synthesizes a z map (I assume from a normal 
distribution) for computing the voxel-wise thresholds and cluster size 
distribution.
Maybe I am wrong with my stats but I wonder if it is ok to use this 
null-hypothesis to a F-distributed data such as results from a F-test.

Thanks!

--
Basile Pinsard
/PhD candidate,
/
Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne 
Universités, UPMC, INSERM, CNRS
/Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne 
Universités
Biomedical Sciences Doctoral School, Faculty of Medicine, Université 
de Montréal

CRIUGM, Université de Montréal


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Re: [Freesurfer] Monte-Carlo correction and 3-groups comparison

[Douglas Greve]

It is appropriate. The F-test is not the same as t-test, so it is not 
totally surpising that you get different results



On 12/22/17 5:06 PM, Pauline Duret wrote:

Hello all,

I am running a gyrification analysis between 3 groups.
So I modeled my GLM like the one on this page: 
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V


I was wondering if it is correct to run a Monte-Carlo correction on 
the results of the Main effect of group (contrast 4 on the page), 
which represents an F test if I am correct.


I use the line mri_glmfit-sim --glmdir Results.rh.00.Groupeffectseul 
--cache 2 abs --cwp 0.05 --2spaces


I get no sig Monte-Carlo corrected results on the main effect of group 
whereas I find interesting sig results in the one-by-one contrast, 
which is a bit surprising.


Thank you for your answer.






———
lnc-autisme.umontreal.ca 
En apprendre plus sur l’autisme:
http://grouperechercheautismemontreal.ca/Magazine.aspx



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[Freesurfer] Monte-Carlo f-test

[basile pinsard]

Hi Freesurfer experts.
Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable for
F-test?
The doc says that it synthesizes a z map (I assume from a  normal
distribution) for computing the voxel-wise thresholds and cluster size
distribution.
Maybe I am wrong with my stats but I wonder if it is ok to use this
null-hypothesis to a F-distributed data such as results from a F-test.
Thanks!

-- 
Basile Pinsard

*PhD candidate, *
Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne
Universités, UPMC, INSERM, CNRS
*Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne
Universités
Biomedical Sciences Doctoral School, Faculty of Medicine, Université de
Montréal
CRIUGM, Université de Montréal
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[Freesurfer] Monte-Carlo correction and 3-groups comparison

[Pauline Duret]

Hello all,

I am running a gyrification analysis between 3 groups.
So I modeled my GLM like the one on this page: 
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V 


I was wondering if it is correct to run a Monte-Carlo correction on the results 
of the Main effect of group (contrast 4 on the page), which represents an F 
test if I am correct.

I use the line mri_glmfit-sim --glmdir Results.rh.00.Groupeffectseul --cache 2 
abs --cwp 0.05 --2spaces

I get no sig Monte-Carlo corrected results on the main effect of group whereas 
I find interesting sig results in the one-by-one contrast, which is a bit 
surprising.

Thank you for your answer.







———
lnc-autisme.umontreal.ca
En apprendre plus sur l’autisme: 
http://grouperechercheautismemontreal.ca/Magazine.aspx 

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Re: [Freesurfer] Monte-Carlo in LME

[Douglas Greve]

yes


On 7/21/17 5:24 AM, Jordi Pegueroles wrote:
> Thank you Doug. So, instead of running mri_surfcluster I should run 
> mri_glmfit-sim with the --fwhm-override with the smoothing obtained 
> from the residuals of the lme model.
>
> Thanks again,
>
> A 2017-07-18 22:09, Douglas N Greve escrigué:
>> Not sure. It might be more accurate. Once you have the FWHM you want,
>> you can run mri_glmfit-sim with --fwhm-override
>>
>>
>> On 07/17/2017 05:43 PM, Jordi Pegueroles wrote:
>>> Dear FS experts,
>>>
>>> I was wondering if someone had performed multiple comparisons (ie 
>>> monte-carlo) with the LME analyses. I have found a thread 
>>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) 
>>> where Doug recommends to run a GLM fit with the same data and then 
>>> overwrite the sig.mgh file with the LME one.
>>>
>>> My question is if is not more accurate to estimate the residuals 
>>> from the LME model, then compute the relative smooth of the data 
>>> with the mris_fwhm command and pass it as an argument in the 
>>> mri_surfcluster command (mri_surfcluster --in $direct1/sig.mgh --csd 
>>> /Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd
>>>  
>>> --cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig 
>>> $direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white).
>>>
>>> Thanks in advance.
>>>
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
>

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Re: [Freesurfer] Monte-Carlo in LME

[Jordi Pegueroles]

Thank you Doug. So, instead of running mri_surfcluster I should run 
mri_glmfit-sim with the --fwhm-override with the smoothing obtained from 
the residuals of the lme model.

Thanks again,

A 2017-07-18 22:09, Douglas N Greve escrigué:
> Not sure. It might be more accurate. Once you have the FWHM you want,
> you can run mri_glmfit-sim with --fwhm-override
> 
> 
> On 07/17/2017 05:43 PM, Jordi Pegueroles wrote:
>> Dear FS experts,
>> 
>> I was wondering if someone had performed multiple comparisons (ie 
>> monte-carlo) with the LME analyses. I have found a thread 
>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) 
>> where Doug recommends to run a GLM fit with the same data and then 
>> overwrite the sig.mgh file with the LME one.
>> 
>> My question is if is not more accurate to estimate the residuals from 
>> the LME model, then compute the relative smooth of the data with the 
>> mris_fwhm command and pass it as an argument in the mri_surfcluster 
>> command (mri_surfcluster --in $direct1/sig.mgh --csd 
>> /Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd
>>  
>> --cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig 
>> $direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white).
>> 
>> Thanks in advance.
>> 
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> 
> 
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.

-- 
Jordi.
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Re: [Freesurfer] Monte-Carlo in LME

[Douglas N Greve]

Not sure. It might be more accurate. Once you have the FWHM you want, 
you can run mri_glmfit-sim with --fwhm-override


On 07/17/2017 05:43 PM, Jordi Pegueroles wrote:
> Dear FS experts,
>
> I was wondering if someone had performed multiple comparisons (ie 
> monte-carlo) with the LME analyses. I have found a thread 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) 
> where Doug recommends to run a GLM fit with the same data and then 
> overwrite the sig.mgh file with the LME one.
>
> My question is if is not more accurate to estimate the residuals from 
> the LME model, then compute the relative smooth of the data with the 
> mris_fwhm command and pass it as an argument in the mri_surfcluster 
> command (mri_surfcluster --in $direct1/sig.mgh --csd 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd
>  
> --cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig 
> $direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white).
>
> Thanks in advance.
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] Monte-Carlo in LME

[Jordi Pegueroles]

Dear FS experts,

I was wondering if someone had performed multiple comparisons (ie 
monte-carlo) with the LME analyses. I have found a thread 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) 
where Doug recommends to run a GLM fit with the same data and then 
overwrite the sig.mgh file with the LME one.

My question is if is not more accurate to estimate the residuals from 
the LME model, then compute the relative smooth of the data with the 
mris_fwhm command and pass it as an argument in the mri_surfcluster 
command (mri_surfcluster --in $direct1/sig.mgh --csd 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd
 
--cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig 
$direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white).

Thanks in advance.

-- 
Jordi.
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Re: [Freesurfer] Monte Carlo error (fwhm4 vs. fwhm04)

[Douglas N Greve]

Hi Eli, I would advise against trying to run MC inside of QDEC. Use 
mri_glmfit-sim instead


On 06/01/2017 04:33 PM, Rockers, Elijah D. wrote:
> Hello FS,
>
> I am attempting to run a monte carlo simulation on some cortical 
> thickness data in Qdec 1.5, but I get the following error:
>
> ERROR: CSDread(): could not open 
> ../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd
>
> I thought it might be a permissions issue since the installation is on 
> an NFS share, but in fact the  .../lh/cortex/fwhm4/ directory 
> does not exist. There is a fwhm04, but not fwhm4. I have two versions 
> of FS installed (5.3 and 6) so I thought it might be referencing the 
> wrong version, but in fact both versions have the same directory 
> structure anyway... Any ideas what is going on?
>
> Thanks,
> - Eli
>
> Houston Methodist. Leading Medicine.
>
> /U.S. News & World Report/ has recognized Houston Methodist as one of 
> the nation’s top 20 hospitals, placing it for the second time on the 
> magazine’s prestigious Honor Roll. It is also designated as a Magnet 
> hospital for excellence in nursing. Visit us at houstonmethodist.org 
> . Follow us at twitter.com/MethodistHosp 
>  and facebook.com/HoustonMethodist.
>
> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston 
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Monte Carlo error (fwhm4 vs. fwhm04)

[Rockers, Elijah D.]

Hello FS,

I am attempting to run a monte carlo simulation on some cortical thickness data 
in Qdec 1.5, but I get the following error:

ERROR: CSDread(): could not open 
../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd

I thought it might be a permissions issue since the installation is on an NFS 
share, but in fact the  .../lh/cortex/fwhm4/ directory does not exist. 
There is a fwhm04, but not fwhm4. I have two versions of FS installed (5.3 and 
6) so I thought it might be referencing the wrong version, but in fact both 
versions have the same directory structure anyway... Any ideas what is going on?

Thanks,
- Eli

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
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Re: [Freesurfer] monte carlo continue/ desktop restarted

[miracle ozzoude]

Thank you

On Wed, Sep 28, 2016 at 3:49 PM, Douglas Greve 
wrote:

> There is no way. Yes, you can specify fsaverage for yoursubject
>
> On 9/28/16 3:47 PM, miracle ozzoude wrote:
>
> Hello Doug,
> Do you know if there's any command to make it continue from where it
> stopped in case of future incidents? Also, what does " yoursubject" mean in
> this code? Can I substitute it with fsaverage?
> Thanks
> Paul
>
> mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/rh/cortex \
>--base mc-z --surface yoursubject rh --nreps 1
>
>
> On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I would just use what was created. There is nothing magical about 10,000
>> iterations. A few iterations short won't make any difference.
>>
>>
>> On 09/28/2016 10:35 AM, miracle ozzoude wrote:
>> > Hello experts,
>> > I was running 1 monte carlo simulation before my desktop
>> > automatically restarted, does anyone know a command to continue from
>> > where it stopped? The simulation for left hemisphere stopped at
>> > 9146/1 and right hemisphere at 9125/1. Thank you
>> > Paul
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
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Re: [Freesurfer] monte carlo continue/ desktop restarted

[Douglas Greve]

There is no way. Yes, you can specify fsaverage for yoursubject


On 9/28/16 3:47 PM, miracle ozzoude wrote:

Hello Doug,
Do you know if there's any command to make it continue from where it 
stopped in case of future incidents? Also, what does " yoursubject" 
mean in this code? Can I substitute it with fsaverage?

Thanks
Paul
mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/rh/cortex \
--base mc-z --surface yoursubject rh --nreps 1

On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve 
> wrote:


I would just use what was created. There is nothing magical about
10,000
iterations. A few iterations short won't make any difference.


On 09/28/2016 10:35 AM, miracle ozzoude wrote:
> Hello experts,
> I was running 1 monte carlo simulation before my desktop
> automatically restarted, does anyone know a command to continue from
> where it stopped? The simulation for left hemisphere stopped at
> 9146/1 and right hemisphere at 9125/1. Thank you
> Paul
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
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gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] monte carlo continue/ desktop restarted

[miracle ozzoude]

Hello Doug,
Do you know if there's any command to make it continue from where it
stopped in case of future incidents? Also, what does " yoursubject" mean in
this code? Can I substitute it with fsaverage?
Thanks
Paul

mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/rh/cortex \
   --base mc-z --surface yoursubject rh --nreps 1


On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve  wrote:

> I would just use what was created. There is nothing magical about 10,000
> iterations. A few iterations short won't make any difference.
>
>
> On 09/28/2016 10:35 AM, miracle ozzoude wrote:
> > Hello experts,
> > I was running 1 monte carlo simulation before my desktop
> > automatically restarted, does anyone know a command to continue from
> > where it stopped? The simulation for left hemisphere stopped at
> > 9146/1 and right hemisphere at 9125/1. Thank you
> > Paul
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] monte carlo continue/ desktop restarted

[miracle ozzoude]

Thank you Doug
Paul

On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve  wrote:

> I would just use what was created. There is nothing magical about 10,000
> iterations. A few iterations short won't make any difference.
>
>
> On 09/28/2016 10:35 AM, miracle ozzoude wrote:
> > Hello experts,
> > I was running 1 monte carlo simulation before my desktop
> > automatically restarted, does anyone know a command to continue from
> > where it stopped? The simulation for left hemisphere stopped at
> > 9146/1 and right hemisphere at 9125/1. Thank you
> > Paul
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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Re: [Freesurfer] monte carlo continue/ desktop restarted

[Douglas N Greve]

I would just use what was created. There is nothing magical about 10,000 
iterations. A few iterations short won't make any difference.


On 09/28/2016 10:35 AM, miracle ozzoude wrote:
> Hello experts,
> I was running 1 monte carlo simulation before my desktop 
> automatically restarted, does anyone know a command to continue from 
> where it stopped? The simulation for left hemisphere stopped at 
> 9146/1 and right hemisphere at 9125/1. Thank you
> Paul
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] monte carlo continue/ desktop restarted

[miracle ozzoude]

Hello experts,
I was running 1 monte carlo simulation before my desktop automatically
restarted, does anyone know a command to continue from where it stopped?
The simulation for left hemisphere stopped at 9146/1 and right
hemisphere at 9125/1. Thank you
Paul
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[Freesurfer] Monte Carlo correction in QDEC

[Clara Kühn]

Dear FreeSurfer experts,

for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.

1. Would I use neg if I have mostly blue clusters in the QDEC display and pos 
if I have mostly red clusters?

2. When do I use abs?

3. I compared the neg option at different thresholds (1.3, 2 and 2.3) and I get 
different clusters:
1.3 (=.05)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  0.00760  
0.01000  1600  superiorfrontal
   2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  0.0  
0.00020  2971  medialorbitofrontal

2.0 (=.01)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  0.01960  
0.02330   571  parsorbitalis
   2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  0.01760  
0.02120   604  superiorfrontal

2.3 (=.005)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  0.01730  
0.02080   410  parsorbitalis

Technically, if parsorbitalis is significant at .01 and .005, shouldn't it also 
be significant at .05? I've compared the clusters in freeview and the 
superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis and 
the medialorbitofrontal clusters are completely different, not even closely 
overlapping.

Do you have any idea why that is and what it does differently?
Thank you!
Cheers, Clara
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Hi DOug,

doug.log is attached

the bash equivalent for |& is 2>&1 |

thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:


I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
sure what the bash equivalent is. Maybe |2 instead of |&
perhaps some bash experts can weigh in

On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:

Hi Doug,

Do you mean:

   mri_glmfit-sim --debug --glmdir 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?

When I tried running the same code with |& tee doug.log at the end, I kept 
getting:

syntax error near unexpected token `&'

Thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:


Can you run

mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
--cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log

and send me doug.log?




On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:

Hi experts,

I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.

My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I 
then ran mri_glmfit on the data.

I want to do my analysis/correction only in auditory cortex (AC) so I did my 
own simulation in AC of each hemisphere using mri_mcsim (as per 
http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).

So far, so good.

But when I try to run:

mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label 
AC --grf 4 neg --cwpvalthresh 0.05 --2space

I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
didn't help.

Any thoughts? Also, can you clarify which comparison neg vs pos will give me?

Thank you,

Susan McLaughlin, PhD
Research Scientist
Laboratory for Auditory Brain Sciences & Neuroengineering
Institute for Learning & Brain Sciences (I-LABS)
Portage Bay Bldg. Room 204
University of Washington, Box 357988
Seattle, WA 98195-7988

Ph: (206) 616-0102 Fx: (206) 221-6472
Cell: 206-850-8638
E-mail: s...@uw.edu


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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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doug.log
Description: Binary data
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

Can you run

mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
--cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log

and send me doug.log?




On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
> Hi experts,
>
> I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
>
> My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. 
> I then ran mri_glmfit on the data.
>
> I want to do my analysis/correction only in auditory cortex (AC) so I did my 
> own simulation in AC of each hemisphere using mri_mcsim (as per 
> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>
> So far, so good.
>
> But when I try to run:
>
> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>
> I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
> didn't help.
>
> Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
>
> Thank you,
>
> Susan McLaughlin, PhD
> Research Scientist
> Laboratory for Auditory Brain Sciences & Neuroengineering
> Institute for Learning & Brain Sciences (I-LABS)
> Portage Bay Bldg. Room 204
> University of Washington, Box 357988
> Seattle, WA 98195-7988
>
> Ph: (206) 616-0102 Fx: (206) 221-6472
> Cell: 206-850-8638
> E-mail: s...@uw.edu
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

I meant &. The & works for tcsh (or csh). Are you using bash? I'm not 
sure what the bash equivalent is. Maybe |2 instead of |&
perhaps some bash experts can weigh in

On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
> Do you mean:
>
>mri_glmfit-sim --debug --glmdir 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>  --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
>
> When I tried running the same code with |& tee doug.log at the end, I kept 
> getting:
>
> syntax error near unexpected token `&'
>
> Thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> Can you run
>>
>> mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
>>
>> and send me doug.log?
>>
>>
>>
>>
>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>>> Hi experts,
>>>
>>> I am having trouble performing a Monte Carlo correction using 
>>> mri_glmfit-sim.
>>>
>>> My data were sampled to fsaverage and smoothed at fwhm 5, using 
>>> mris_preproc. I then ran mri_glmfit on the data.
>>>
>>> I want to do my analysis/correction only in auditory cortex (AC) so I did 
>>> my own simulation in AC of each hemisphere using mri_mcsim (as per 
>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>>
>>> So far, so good.
>>>
>>> But when I try to run:
>>>
>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>>
>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
>>> didn't help.
>>>
>>> Any thoughts? Also, can you clarify which comparison neg vs pos will give 
>>> me?
>>>
>>> Thank you,
>>>
>>> Susan McLaughlin, PhD
>>> Research Scientist
>>> Laboratory for Auditory Brain Sciences & Neuroengineering
>>> Institute for Learning & Brain Sciences (I-LABS)
>>> Portage Bay Bldg. Room 204
>>> University of Washington, Box 357988
>>> Seattle, WA 98195-7988
>>>
>>> Ph: (206) 616-0102 Fx: (206) 221-6472
>>> Cell: 206-850-8638
>>> E-mail: s...@uw.edu
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

it cannot find this file

/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat

which should have been created by mri_glmfit. What is your mri_glmfit 
command line?

Also, don't use --grf, that is for volumes only


On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
> Hi DOug,
>
> doug.log is attached
>
> the bash equivalent for |& is 2>&1 |
>
> thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
>> sure what the bash equivalent is. Maybe |2 instead of |&
>> perhaps some bash experts can weigh in
>>
>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
>>> Hi Doug,
>>>
>>> Do you mean:
>>>
>>>mri_glmfit-sim --debug --glmdir 
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>>>  
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee 
>>> doug.log?
>>>
>>> When I tried running the same code with |& tee doug.log at the end, 
>>> I kept getting:
>>>
>>> syntax error near unexpected token `&'
>>>
>>> Thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 Can you run

 mri_glmfit-sim --debug --glmdir [my data 
 dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg 
 --cwpvalthresh 0.05 --2space |& tee doug.log

 and send me doug.log?




 On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
> Hi experts,
>
> I am having trouble performing a Monte Carlo correction using 
> mri_glmfit-sim.
>
> My data were sampled to fsaverage and smoothed at fwhm 5, using 
> mris_preproc. I then ran mri_glmfit on the data.
>
> I want to do my analysis/correction only in auditory cortex (AC) 
> so I did my own simulation in AC of each hemisphere using 
> mri_mcsim (as per 
> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>
> So far, so good.
>
> But when I try to run:
>
> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>
> I get "fwhm: Undefined variable." I tried adding --fwhm-override 
> 5, but it didn't help.
>
> Any thoughts? Also, can you clarify which comparison neg vs pos 
> will give me?
>
> Thank you,
>
> Susan McLaughlin, PhD
> Research Scientist
> Laboratory for Auditory Brain Sciences & Neuroengineering
> Institute for Learning & Brain Sciences (I-LABS)
> Portage Bay Bldg. Room 204
> University of Washington, Box 357988
> Seattle, WA 98195-7988
>
> Ph: (206) 616-0102 Fx: (206) 221-6472
> Cell: 206-850-8638
> E-mail: s...@uw.edu
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to 
 whom it is
 addressed. If you believe this e-mail was sent to you in error and 
 the e-mail
 contains patient information, please contact the Partners 
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to 
 you in error
 but does not contain patient information, please contact the sender 
 and properly
 dispose of the e-mail.


>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Hi Doug,

Do you mean:

  mri_glmfit-sim --debug --glmdir 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?

When I tried running the same code with |& tee doug.log at the end, I kept 
getting:

syntax error near unexpected token `&'

Thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

>
> Can you run
>
> mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
>
> and send me doug.log?
>
>
>
>
> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>> Hi experts,
>>
>> I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
>>
>> My data were sampled to fsaverage and smoothed at fwhm 5, using 
>> mris_preproc. I then ran mri_glmfit on the data.
>>
>> I want to do my analysis/correction only in auditory cortex (AC) so I did my 
>> own simulation in AC of each hemisphere using mri_mcsim (as per 
>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>
>> So far, so good.
>>
>> But when I try to run:
>>
>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>
>> I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
>> didn't help.
>>
>> Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
>>
>> Thank you,
>>
>> Susan McLaughlin, PhD
>> Research Scientist
>> Laboratory for Auditory Brain Sciences & Neuroengineering
>> Institute for Learning & Brain Sciences (I-LABS)
>> Portage Bay Bldg. Room 204
>> University of Washington, Box 357988
>> Seattle, WA 98195-7988
>>
>> Ph: (206) 616-0102 Fx: (206) 221-6472
>> Cell: 206-850-8638
>> E-mail: s...@uw.edu
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>

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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

I am using bash. I am trying to google the bash equivalent of tcsh |&, but if 
anybody knows it, please let me know.

thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
> sure what the bash equivalent is. Maybe |2 instead of |&
> perhaps some bash experts can weigh in
>
> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
>> Hi Doug,
>>
>> Do you mean:
>>
>>mri_glmfit-sim --debug --glmdir 
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>>  --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
>>
>> When I tried running the same code with |& tee doug.log at the end, I kept 
>> getting:
>>
>> syntax error near unexpected token `&'
>>
>> Thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> Can you run
>>>
>>> mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
>>>
>>> and send me doug.log?
>>>
>>>
>>>
>>>
>>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
 Hi experts,

 I am having trouble performing a Monte Carlo correction using 
 mri_glmfit-sim.

 My data were sampled to fsaverage and smoothed at fwhm 5, using 
 mris_preproc. I then ran mri_glmfit on the data.

 I want to do my analysis/correction only in auditory cortex (AC) so I did 
 my own simulation in AC of each hemisphere using mri_mcsim (as per 
 http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).

 So far, so good.

 But when I try to run:

 mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space

 I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
 didn't help.

 Any thoughts? Also, can you clarify which comparison neg vs pos will give 
 me?

 Thank you,

 Susan McLaughlin, PhD
 Research Scientist
 Laboratory for Auditory Brain Sciences & Neuroengineering
 Institute for Learning & Brain Sciences (I-LABS)
 Portage Bay Bldg. Room 204
 University of Washington, Box 357988
 Seattle, WA 98195-7988

 Ph: (206) 616-0102 Fx: (206) 221-6472
 Cell: 206-850-8638
 E-mail: s...@uw.edu


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in 
[mydata}/cope7ACroi_rh.osgm.rfx.

There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), and 
even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, gammavar, 
mask, and sig) but no rh.cope7.mgh.

Thanks for going back and forth about this,

Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

> The correct command line is
>
> --cache 4 neg --cache-label AC
>
> On 11/03/2015 03:36 PM, s...@u.washington.edu wrote:
>> Hi Doug,
>>
>>
>>
>> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot
>> find any documentation about what to put instead of --grf), as in
>>
>> mri_glmfit-sim --glmdir
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx
>> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
>>
>> I get back "ERROR: Flag 4 is unrecognized."
>>
>> If I try just --cache instead of --cache-label AC, I get back "ERROR:
>> cannot find
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
>>
>> Any thoughts?
>>
>> Many thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> The fwhm.dat file was in the right place. You passed the wrong folder to
>>> mri_glmfit-sim. You should pass it
>>>
>>> cope7ACroi_rh.osgm.rfx
>>>
>>> doug
>>>
>>>
>>> On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
 It's:

 mri_glmfit --y
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh
 --osgm --glmdir
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
 --surf fsaverage lh --label
 /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label

 fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than
 [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also
 happened for some other files needed and I moved them. Is the
 problem something in my mri_glmfit command?

 Susan

 On Tue, 3 Nov 2015, Douglas N Greve wrote:

> it cannot find this file
>
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>
>
> which should have been created by mri_glmfit. What is your mri_glmfit
> command line?
>
> Also, don't use --grf, that is for volumes only
>
>
> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>> Hi DOug,
>>
>> doug.log is attached
>>
>> the bash equivalent for |& is 2>&1 |
>>
>> thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm
>>> not
>>> sure what the bash equivalent is. Maybe |2 instead of |&
>>> perhaps some bash experts can weigh in
>>>
>>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
 Hi Doug,

 Do you mean:

 mri_glmfit-sim --debug --glmdir
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm

 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
 doug.log?

 When I tried running the same code with |& tee doug.log at the end,
 I kept getting:

 syntax error near unexpected token `&'

 Thanks,
 Susan

 On Tue, 3 Nov 2015, Douglas N Greve wrote:

> Can you run
>
> mri_glmfit-sim --debug --glmdir [my data
> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
> --cwpvalthresh 0.05 --2space |& tee doug.log
>
> and send me doug.log?
>
>
>
>
> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>> Hi experts,
>>
>> I am having trouble performing a Monte Carlo correction using
>> mri_glmfit-sim.
>>
>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>> mris_preproc. I then ran mri_glmfit on the data.
>>
>> I want to do my analysis/correction only in auditory cortex (AC)
>> so I did my own simulation in AC of each hemisphere using
>> mri_mcsim (as per
>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>
>> So far, so good.
>>
>> But when I try to run:
>>
>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>
>> I get "fwhm: Undefined variable." I tried adding --fwhm-override
>> 5, but it didn't help.
>>
>> Any thoughts? Also, can you clarify which comparison neg vs pos
>> will give me?
>>
>> Thank you,
>>
>> Susan McLaughlin, PhD
>> Research Scientist
>> Laboratory for Auditory Brain 

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

The correct command line is

--cache 4 neg --cache-label AC

On 11/03/2015 03:36 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
>
>
> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot 
> find any documentation about what to put instead of --grf), as in
>
> mri_glmfit-sim --glmdir 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx 
> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
>
> I get back "ERROR: Flag 4 is unrecognized."
>
> If I try just --cache instead of --cache-label AC, I get back "ERROR: 
> cannot find 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
>
> Any thoughts?
>
> Many thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> The fwhm.dat file was in the right place. You passed the wrong folder to
>> mri_glmfit-sim. You should pass it
>>
>> cope7ACroi_rh.osgm.rfx
>>
>> doug
>>
>>
>> On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
>>> It's:
>>>
>>> mri_glmfit --y 
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh 
>>> --osgm --glmdir 
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
>>>  
>>> --surf fsaverage lh --label 
>>> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
>>>
>>> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than 
>>> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also 
>>> happened for some other files needed and I moved them. Is the 
>>> problem something in my mri_glmfit command?
>>>
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 it cannot find this file

 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
  


 which should have been created by mri_glmfit. What is your mri_glmfit
 command line?

 Also, don't use --grf, that is for volumes only


 On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
> Hi DOug,
>
> doug.log is attached
>
> the bash equivalent for |& is 2>&1 |
>
> thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm 
>> not
>> sure what the bash equivalent is. Maybe |2 instead of |&
>> perhaps some bash experts can weigh in
>>
>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
>>> Hi Doug,
>>>
>>> Do you mean:
>>>
>>> mri_glmfit-sim --debug --glmdir
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>>>  
>>>
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
>>> doug.log?
>>>
>>> When I tried running the same code with |& tee doug.log at the end,
>>> I kept getting:
>>>
>>> syntax error near unexpected token `&'
>>>
>>> Thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 Can you run

 mri_glmfit-sim --debug --glmdir [my data
 dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
 --cwpvalthresh 0.05 --2space |& tee doug.log

 and send me doug.log?




 On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
> Hi experts,
>
> I am having trouble performing a Monte Carlo correction using
> mri_glmfit-sim.
>
> My data were sampled to fsaverage and smoothed at fwhm 5, using
> mris_preproc. I then ran mri_glmfit on the data.
>
> I want to do my analysis/correction only in auditory cortex (AC)
> so I did my own simulation in AC of each hemisphere using
> mri_mcsim (as per
> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>
> So far, so good.
>
> But when I try to run:
>
> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>
> I get "fwhm: Undefined variable." I tried adding --fwhm-override
> 5, but it didn't help.
>
> Any thoughts? Also, can you clarify which comparison neg vs pos
> will give me?
>
> Thank you,
>
> Susan McLaughlin, PhD
> Research Scientist
> Laboratory for Auditory Brain Sciences & Neuroengineering
> Institute for Learning & Brain Sciences (I-LABS)
> Portage Bay Bldg. Room 204
> University of Washington, Box 357988
> Seattle, WA 98195-7988
>
> Ph: (206) 616-0102 Fx: (206) 221-6472
> Cell: 206-850-8638
> E-mail: s...@uw.edu
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

The fwhm.dat file was in the right place. You passed the wrong folder to 
mri_glmfit-sim. You should pass it

cope7ACroi_rh.osgm.rfx

doug


On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
> It's:
>
> mri_glmfit --y 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh 
> --osgm --glmdir 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
>  --surf fsaverage lh --label 
> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
>
> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than 
> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for 
> some other files needed and I moved them. Is the problem something in my 
> mri_glmfit command?
>
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> it cannot find this file
>>
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>>
>> which should have been created by mri_glmfit. What is your mri_glmfit
>> command line?
>>
>> Also, don't use --grf, that is for volumes only
>>
>>
>> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>>> Hi DOug,
>>>
>>> doug.log is attached
>>>
>>> the bash equivalent for |& is 2>&1 |
>>>
>>> thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
 sure what the bash equivalent is. Maybe |2 instead of |&
 perhaps some bash experts can weigh in

 On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
> Do you mean:
>
> mri_glmfit-sim --debug --glmdir
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
> doug.log?
>
> When I tried running the same code with |& tee doug.log at the end,
> I kept getting:
>
> syntax error near unexpected token `&'
>
> Thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> Can you run
>>
>> mri_glmfit-sim --debug --glmdir [my data
>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
>> --cwpvalthresh 0.05 --2space |& tee doug.log
>>
>> and send me doug.log?
>>
>>
>>
>>
>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>>> Hi experts,
>>>
>>> I am having trouble performing a Monte Carlo correction using
>>> mri_glmfit-sim.
>>>
>>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>>> mris_preproc. I then ran mri_glmfit on the data.
>>>
>>> I want to do my analysis/correction only in auditory cortex (AC)
>>> so I did my own simulation in AC of each hemisphere using
>>> mri_mcsim (as per
>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>>
>>> So far, so good.
>>>
>>> But when I try to run:
>>>
>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>>
>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override
>>> 5, but it didn't help.
>>>
>>> Any thoughts? Also, can you clarify which comparison neg vs pos
>>> will give me?
>>>
>>> Thank you,
>>>
>>> Susan McLaughlin, PhD
>>> Research Scientist
>>> Laboratory for Auditory Brain Sciences & Neuroengineering
>>> Institute for Learning & Brain Sciences (I-LABS)
>>> Portage Bay Bldg. Room 204
>>> University of Washington, Box 357988
>>> Seattle, WA 98195-7988
>>>
>>> Ph: (206) 616-0102 Fx: (206) 221-6472
>>> Cell: 206-850-8638
>>> E-mail: s...@uw.edu
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> 

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

It's:

mri_glmfit --y 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm 
--glmdir 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
 --surf fsaverage lh --label 
/Applications/freesurfer/subjects/fsaverage/label/lh.AC.label

fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than 
[MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for 
some other files needed and I moved them. Is the problem something in my 
mri_glmfit command?

Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

>
> it cannot find this file
>
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>
> which should have been created by mri_glmfit. What is your mri_glmfit
> command line?
>
> Also, don't use --grf, that is for volumes only
>
>
> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>> Hi DOug,
>>
>> doug.log is attached
>>
>> the bash equivalent for |& is 2>&1 |
>>
>> thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
>>> sure what the bash equivalent is. Maybe |2 instead of |&
>>> perhaps some bash experts can weigh in
>>>
>>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
 Hi Doug,

 Do you mean:

mri_glmfit-sim --debug --glmdir
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
 doug.log?

 When I tried running the same code with |& tee doug.log at the end,
 I kept getting:

 syntax error near unexpected token `&'

 Thanks,
 Susan

 On Tue, 3 Nov 2015, Douglas N Greve wrote:

> Can you run
>
> mri_glmfit-sim --debug --glmdir [my data
> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
> --cwpvalthresh 0.05 --2space |& tee doug.log
>
> and send me doug.log?
>
>
>
>
> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>> Hi experts,
>>
>> I am having trouble performing a Monte Carlo correction using
>> mri_glmfit-sim.
>>
>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>> mris_preproc. I then ran mri_glmfit on the data.
>>
>> I want to do my analysis/correction only in auditory cortex (AC)
>> so I did my own simulation in AC of each hemisphere using
>> mri_mcsim (as per
>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>
>> So far, so good.
>>
>> But when I try to run:
>>
>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>
>> I get "fwhm: Undefined variable." I tried adding --fwhm-override
>> 5, but it didn't help.
>>
>> Any thoughts? Also, can you clarify which comparison neg vs pos
>> will give me?
>>
>> Thank you,
>>
>> Susan McLaughlin, PhD
>> Research Scientist
>> Laboratory for Auditory Brain Sciences & Neuroengineering
>> Institute for Learning & Brain Sciences (I-LABS)
>> Portage Bay Bldg. Room 204
>> University of Washington, Box 357988
>> Seattle, WA 98195-7988
>>
>> Ph: (206) 616-0102 Fx: (206) 221-6472
>> Cell: 206-850-8638
>> E-mail: s...@uw.edu
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>>
>>> --
>>> Douglas N. Greve, 

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

When you ran mri_glmfit the first time, you had to specify a file with 
the --y flag. It is looking for that file now. Does that file still 
exist in the location where it was when you ran mri_glmfit?


On 11/03/2015 04:50 PM, s...@u.washington.edu wrote:
> Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in 
> [mydata}/cope7ACroi_rh.osgm.rfx.
>
> There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), 
> and even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, 
> gammavar, mask, and sig) but no rh.cope7.mgh.
>
> Thanks for going back and forth about this,
>
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> The correct command line is
>>
>> --cache 4 neg --cache-label AC
>>
>> On 11/03/2015 03:36 PM, s...@u.washington.edu wrote:
>>> Hi Doug,
>>>
>>>
>>>
>>> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot
>>> find any documentation about what to put instead of --grf), as in
>>>
>>> mri_glmfit-sim --glmdir
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx
>>> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
>>>
>>> I get back "ERROR: Flag 4 is unrecognized."
>>>
>>> If I try just --cache instead of --cache-label AC, I get back "ERROR:
>>> cannot find
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
>>>
>>> Any thoughts?
>>>
>>> Many thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 The fwhm.dat file was in the right place. You passed the wrong folder to
 mri_glmfit-sim. You should pass it

 cope7ACroi_rh.osgm.rfx

 doug


 On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
> It's:
>
> mri_glmfit --y
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh
> --osgm --glmdir
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
> --surf fsaverage lh --label
> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
>
> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than
> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also
> happened for some other files needed and I moved them. Is the
> problem something in my mri_glmfit command?
>
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> it cannot find this file
>>
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>>
>>
>> which should have been created by mri_glmfit. What is your mri_glmfit
>> command line?
>>
>> Also, don't use --grf, that is for volumes only
>>
>>
>> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>>> Hi DOug,
>>>
>>> doug.log is attached
>>>
>>> the bash equivalent for |& is 2>&1 |
>>>
>>> thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 I meant &. The & works for tcsh (or csh). Are you using bash? I'm
 not
 sure what the bash equivalent is. Maybe |2 instead of |&
 perhaps some bash experts can weigh in

 On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
> Do you mean:
>
>  mri_glmfit-sim --debug --glmdir
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
> doug.log?
>
> When I tried running the same code with |& tee doug.log at the end,
> I kept getting:
>
> syntax error near unexpected token `&'
>
> Thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> Can you run
>>
>> mri_glmfit-sim --debug --glmdir [my data
>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
>> --cwpvalthresh 0.05 --2space |& tee doug.log
>>
>> and send me doug.log?
>>
>>
>>
>>
>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>>> Hi experts,
>>>
>>> I am having trouble performing a Monte Carlo correction using
>>> mri_glmfit-sim.
>>>
>>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>>> mris_preproc. I then ran mri_glmfit on the data.
>>>
>>> I want to do my analysis/correction only in auditory cortex (AC)
>>> so I did my own simulation in AC of each hemisphere using
>>> mri_mcsim (as per
>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>>
>>> So far, so good.
>>>
>>> But when I try to run:
>>>
>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>>> --cache-label AC --grf 4 

[Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Hi experts,

I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.

My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I 
then ran mri_glmfit on the data.

I want to do my analysis/correction only in auditory cortex (AC) so I did my 
own simulation in AC of each hemisphere using mri_mcsim (as per 
http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).

So far, so good.

But when I try to run:

mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label 
AC --grf 4 neg --cwpvalthresh 0.05 --2space

I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
didn't help.

Any thoughts? Also, can you clarify which comparison neg vs pos will give me?

Thank you,

Susan McLaughlin, PhD
Research Scientist
Laboratory for Auditory Brain Sciences & Neuroengineering
Institute for Learning & Brain Sciences (I-LABS)
Portage Bay Bldg. Room 204
University of Washington, Box 357988
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Ph: (206) 616-0102 Fx: (206) 221-6472
Cell: 206-850-8638
E-mail: s...@uw.edu


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Re: [Freesurfer] Monte Carlo correction

[Douglas Greve]

No, QDEC is a very limited tool. You'll have to use the command line 
(mri_glmfit-sim). Also, you'll need to register each of your subjects to 
the new atlas (surfreg), then specify the average subject AND the new 
registration when running mris_preproc to create a new y.mgh file. None 
of this can be done in qdec.


doug

On 8/27/15 10:21 AM, Kai Jannusch wrote:


Dear all,

During my analysis for pial_lgi instead of using fsaverage I prepared 
my own average surface using make_average and recon-all qcache. Now, I 
want to correct the results for multiple comparisons using Monte Carlo 
Null-Z simulation in Qdec. However, when I use my own average as 
common-space subject it doesn´t work.


My proceeding:

preparation of my own average: make_average and recon-all qcache

run a parallelized Monte Carlo simulation for all subjects separated 
in 10 spaces: mri_mcsim


merge the outputs of the simulation in two mc-z.cdf (one for each 
hemisphere) files


Is there a command that Qdec can use the new Monte Carlo files for my 
dataset?


If not. Is there a possibility to run a Monte Carlo correction with my 
dataset?


Thanks for your ideas!

KJ, CJ



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Monte Carlo correction

[Kai Jannusch]

Dear all,

During my analysis for pial_lgi instead of using fsaverage I prepared my 
own average surface using make_average and recon-all qcache. Now, I want 
to correct the results for multiple comparisons using Monte Carlo Null-Z 
simulation in Qdec. However, when I use my own average as common-space 
subject it doesn´t work.


My proceeding:

preparation of my own average: make_average and recon-all qcache

run a parallelized Monte Carlo simulation for all subjects separated in 
10 spaces: mri_mcsim


merge the outputs of the simulation in two mc-z.cdf (one for each 
hemisphere) files


Is there a command that Qdec can use the new Monte Carlo files for my 
dataset?


If not. Is there a possibility to run a Monte Carlo correction with my 
dataset?


Thanks for your ideas!

KJ, CJ

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

Ok! Can I still use these masks as long as I know what areas are interpretable? 
If so, what does it mean in terms of my original question (limiting the MCS to 
subcortical structures)?
 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, March 12, 2015 10:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

Yes, that probably is the reason.
doug

On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
 To be honest, I checked the between subject alignment and it looked pretty 
 good. None of my subjects was way out of alignment. However, since we cannot 
 fit the whole brain in the slice during scanning, we are always cutting of 
 the top of the brain, sometimes more, sometimes less, depending on the brain 
 size. Could this be the reason why the mask is off? If not, is there anything 
 else I can check?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 2:47 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I meant which ones are causing the problems when you run mri_glmfit.
 When you run fslview you will see something that looks like a brain. As
 you scroll thru the different time points, you'll see the CBF maps for
 different subjects. They should be more-or-less in alignment. Look for
 ones that are way out of alignment or don't have all of the brain.

 On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote:
 Well, I checked the proper match of ASL and anatomical scans again and one 
 of the subjects I reported before was indeed wrongly matched. Thanks!

 What do you mean with So the next thing I would do is to find which 
 subjects are the
 ones that are off.? You mean off when I check for registration? That's what 
 I did before with tkregister2 and they all looked fine to me. What do I look 
 for when I open the cbf.talaraich.nii.gz file in fslview?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 12:19 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 If the registration looks ok, then that is all that counts. However, I'm
 a bit sceptical that the reg looks ok but the mincost is that much
 different than the others. You should double check that the ASL is
 properly matched with the corresponding anatomical (ie, it is not two
 different subjects). This would also not explain why the masks were so
 far off. So the next thing I would do is to find which subjects are the
 ones that are off. You can do this with something like

 fslview y.nii.gz

 where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
 (you can mri_convert it to nii.gz). You can then step through each frame
 (or play them as a movie) to see if any look odd.

 The mincost is from the BBR cost function. It is basically the mean
 gray/white contrast across cortex passed through a sigmoid function to
 make its range 0-1, 0 being best. You cannot necessarily generalize the
 normal range for one modality to that of another.


 On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed 
 them with the tkregister 2 command, with values of .9 and higher (all the 
 other subjects had values between .44 and .61). Do you recommend to redo 
 the analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first 
 value in the .mincost file generated and what does it mean? Can you use 
 this file for other modalities, too? Let's say if I want to do the first 
 level analysis for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

When you run mri_glmfit, add --mask 
$SUBJECTS_DIR/fsaverage/mri.2mm/subcort.mask.mgz

doug

On 03/13/2015 11:17 AM, Wolthusen, Rick Peter Fritz wrote:
 Ok! Can I still use these masks as long as I know what areas are 
 interpretable? If so, what does it mean in terms of my original question 
 (limiting the MCS to subcortical structures)?
   
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 10:29 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Yes, that probably is the reason.
 doug

 On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
 To be honest, I checked the between subject alignment and it looked pretty 
 good. None of my subjects was way out of alignment. However, since we cannot 
 fit the whole brain in the slice during scanning, we are always cutting of 
 the top of the brain, sometimes more, sometimes less, depending on the brain 
 size. Could this be the reason why the mask is off? If not, is there 
 anything else I can check?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 2:47 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I meant which ones are causing the problems when you run mri_glmfit.
 When you run fslview you will see something that looks like a brain. As
 you scroll thru the different time points, you'll see the CBF maps for
 different subjects. They should be more-or-less in alignment. Look for
 ones that are way out of alignment or don't have all of the brain.

 On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote:
 Well, I checked the proper match of ASL and anatomical scans again and one 
 of the subjects I reported before was indeed wrongly matched. Thanks!

 What do you mean with So the next thing I would do is to find which 
 subjects are the
 ones that are off.? You mean off when I check for registration? That's 
 what I did before with tkregister2 and they all looked fine to me. What do 
 I look for when I open the cbf.talaraich.nii.gz file in fslview?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 12:19 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 If the registration looks ok, then that is all that counts. However, I'm
 a bit sceptical that the reg looks ok but the mincost is that much
 different than the others. You should double check that the ASL is
 properly matched with the corresponding anatomical (ie, it is not two
 different subjects). This would also not explain why the masks were so
 far off. So the next thing I would do is to find which subjects are the
 ones that are off. You can do this with something like

 fslview y.nii.gz

 where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
 (you can mri_convert it to nii.gz). You can then step through each frame
 (or play them as a movie) to see if any look odd.

 The mincost is from the BBR cost function. It is basically the mean
 gray/white contrast across cortex passed through a sigmoid function to
 make its range 0-1, 0 being best. You cannot necessarily generalize the
 normal range for one modality to that of another.


 On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed 
 them with the tkregister 2 command, with values of .9 and higher (all the 
 other subjects had values between .44 and .61). Do you recommend to redo 
 the analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first 
 value in the .mincost file generated and what does it mean? Can you use 
 this file for other modalities, too? Let's say if I want to do the first 
 level analysis for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

Sorry, I don't have time to deconstruct that script. Can you simplify it 
for me?

On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, the 
 only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] Monte Carlo Simulation

[Douglas Greve]

Yes, that probably is the reason.
doug

On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
 To be honest, I checked the between subject alignment and it looked pretty 
 good. None of my subjects was way out of alignment. However, since we cannot 
 fit the whole brain in the slice during scanning, we are always cutting of 
 the top of the brain, sometimes more, sometimes less, depending on the brain 
 size. Could this be the reason why the mask is off? If not, is there anything 
 else I can check?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 2:47 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I meant which ones are causing the problems when you run mri_glmfit.
 When you run fslview you will see something that looks like a brain. As
 you scroll thru the different time points, you'll see the CBF maps for
 different subjects. They should be more-or-less in alignment. Look for
 ones that are way out of alignment or don't have all of the brain.

 On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote:
 Well, I checked the proper match of ASL and anatomical scans again and one 
 of the subjects I reported before was indeed wrongly matched. Thanks!

 What do you mean with So the next thing I would do is to find which 
 subjects are the
 ones that are off.? You mean off when I check for registration? That's what 
 I did before with tkregister2 and they all looked fine to me. What do I look 
 for when I open the cbf.talaraich.nii.gz file in fslview?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 12:19 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 If the registration looks ok, then that is all that counts. However, I'm
 a bit sceptical that the reg looks ok but the mincost is that much
 different than the others. You should double check that the ASL is
 properly matched with the corresponding anatomical (ie, it is not two
 different subjects). This would also not explain why the masks were so
 far off. So the next thing I would do is to find which subjects are the
 ones that are off. You can do this with something like

 fslview y.nii.gz

 where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
 (you can mri_convert it to nii.gz). You can then step through each frame
 (or play them as a movie) to see if any look odd.

 The mincost is from the BBR cost function. It is basically the mean
 gray/white contrast across cortex passed through a sigmoid function to
 make its range 0-1, 0 being best. You cannot necessarily generalize the
 normal range for one modality to that of another.


 On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed 
 them with the tkregister 2 command, with values of .9 and higher (all the 
 other subjects had values between .44 and .61). Do you recommend to redo 
 the analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first 
 value in the .mincost file generated and what does it mean? Can you use 
 this file for other modalities, too? Let's say if I want to do the first 
 level analysis for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value in the aslcal.reg.mincost  file. What is the 
 normal range? Also, I don't understand what you mean with the FSL 
 initialization fails and try --init-spm - can you please give me some 
 more information? Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

If the registration looks ok, then that is all that counts. However, I'm 
a bit sceptical that the reg looks ok but the mincost is that much 
different than the others. You should double check that the ASL is 
properly matched with the corresponding anatomical (ie, it is not two 
different subjects). This would also not explain why the masks were so 
far off. So the next thing I would do is to find which subjects are the 
ones that are off. You can do this with something like

fslview y.nii.gz

where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit 
(you can mri_convert it to nii.gz). You can then step through each frame 
(or play them as a movie) to see if any look odd.

The mincost is from the BBR cost function. It is basically the mean 
gray/white contrast across cortex passed through a sigmoid function to 
make its range 0-1, 0 being best. You cannot necessarily generalize the 
normal range for one modality to that of another.


On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed them 
 with the tkregister 2 command, with values of .9 and higher (all the other 
 subjects had values between .44 and .61). Do you recommend to redo the 
 analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first value 
 in the .mincost file generated and what does it mean? Can you use this file 
 for other modalities, too? Let's say if I want to do the first level analysis 
 for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value in the aslcal.reg.mincost  file. What is the normal 
 range? Also, I don't understand what you mean with the FSL initialization 
 fails and try --init-spm - can you please give me some more information? 
 Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Try checking the individual registrations (or look at the first value in
 the .mincost file) to find subjects whose registration may have been off
 and so causes the final mask to be non-sense. Sometimes the FSL
 initialization fails. If so, you might try it with --init-spm


 On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I still can't really tell what it is doing. It looks like it is just
 concatenating several input files that are passed on the command line.
 how were those created?


 On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

Hi Doug et al.,

I indeed found 3 subjects, whose registration looked ok when I eyeballed them 
with the tkregister 2 command, with values of .9 and higher (all the other 
subjects had values between .44 and .61). Do you recommend to redo the analysis 
without them or to run the first level analysis again with --init-spm instead 
of --init-fsl in bbregister? Also, how is the first value in the .mincost file 
generated and what does it mean? Can you use this file for other modalities, 
too? Let's say if I want to do the first level analysis for fct. connectivity 
instead of PASL for example?

Thanks,
Rick

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11, 2015 6:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

For the range, lower is better, but it impossible to say exactly what is
good enough because it depends on your data. If it is 0.8 or higher,
then that is probably bad. What I'm hoping is that there will be one or
two outliers. The --init-spm was in place of --init-fsl in bbregister.
But you only need that if you find a bad registration.

On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and look 
 at the first value in the aslcal.reg.mincost  file. What is the normal range? 
 Also, I don't understand what you mean with the FSL initialization fails 
 and try --init-spm - can you please give me some more information? Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Try checking the individual registrations (or look at the first value in
 the .mincost file) to find subjects whose registration may have been off
 and so causes the final mask to be non-sense. Sometimes the FSL
 initialization fails. If so, you might try it with --init-spm


 On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I still can't really tell what it is doing. It looks like it is just
 concatenating several input files that are passed on the command line.
 how were those created?


 On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers 
 to the above mentioned mask with regards to the used Mask Vol

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

To be honest, I checked the between subject alignment and it looked pretty 
good. None of my subjects was way out of alignment. However, since we cannot 
fit the whole brain in the slice during scanning, we are always cutting of the 
top of the brain, sometimes more, sometimes less, depending on the brain size. 
Could this be the reason why the mask is off? If not, is there anything else I 
can check?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, March 12, 2015 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

I meant which ones are causing the problems when you run mri_glmfit.
When you run fslview you will see something that looks like a brain. As
you scroll thru the different time points, you'll see the CBF maps for
different subjects. They should be more-or-less in alignment. Look for
ones that are way out of alignment or don't have all of the brain.

On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote:
 Well, I checked the proper match of ASL and anatomical scans again and one of 
 the subjects I reported before was indeed wrongly matched. Thanks!

 What do you mean with So the next thing I would do is to find which subjects 
 are the
 ones that are off.? You mean off when I check for registration? That's what 
 I did before with tkregister2 and they all looked fine to me. What do I look 
 for when I open the cbf.talaraich.nii.gz file in fslview?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 12:19 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 If the registration looks ok, then that is all that counts. However, I'm
 a bit sceptical that the reg looks ok but the mincost is that much
 different than the others. You should double check that the ASL is
 properly matched with the corresponding anatomical (ie, it is not two
 different subjects). This would also not explain why the masks were so
 far off. So the next thing I would do is to find which subjects are the
 ones that are off. You can do this with something like

 fslview y.nii.gz

 where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
 (you can mri_convert it to nii.gz). You can then step through each frame
 (or play them as a movie) to see if any look odd.

 The mincost is from the BBR cost function. It is basically the mean
 gray/white contrast across cortex passed through a sigmoid function to
 make its range 0-1, 0 being best. You cannot necessarily generalize the
 normal range for one modality to that of another.


 On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed 
 them with the tkregister 2 command, with values of .9 and higher (all the 
 other subjects had values between .44 and .61). Do you recommend to redo the 
 analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first value 
 in the .mincost file generated and what does it mean? Can you use this file 
 for other modalities, too? Let's say if I want to do the first level 
 analysis for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value in the aslcal.reg.mincost  file. What is the normal 
 range? Also, I don't understand what you mean with the FSL initialization 
 fails and try --init-spm - can you please give me some more information? 
 Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Try checking the individual registrations (or look at the first value in
 the .mincost file

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

I meant which ones are causing the problems when you run mri_glmfit. 
When you run fslview you will see something that looks like a brain. As 
you scroll thru the different time points, you'll see the CBF maps for 
different subjects. They should be more-or-less in alignment. Look for 
ones that are way out of alignment or don't have all of the brain.

On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote:
 Well, I checked the proper match of ASL and anatomical scans again and one of 
 the subjects I reported before was indeed wrongly matched. Thanks!

 What do you mean with So the next thing I would do is to find which subjects 
 are the
 ones that are off.? You mean off when I check for registration? That's what 
 I did before with tkregister2 and they all looked fine to me. What do I look 
 for when I open the cbf.talaraich.nii.gz file in fslview?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, March 12, 2015 12:19 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 If the registration looks ok, then that is all that counts. However, I'm
 a bit sceptical that the reg looks ok but the mincost is that much
 different than the others. You should double check that the ASL is
 properly matched with the corresponding anatomical (ie, it is not two
 different subjects). This would also not explain why the masks were so
 far off. So the next thing I would do is to find which subjects are the
 ones that are off. You can do this with something like

 fslview y.nii.gz

 where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
 (you can mri_convert it to nii.gz). You can then step through each frame
 (or play them as a movie) to see if any look odd.

 The mincost is from the BBR cost function. It is basically the mean
 gray/white contrast across cortex passed through a sigmoid function to
 make its range 0-1, 0 being best. You cannot necessarily generalize the
 normal range for one modality to that of another.


 On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed 
 them with the tkregister 2 command, with values of .9 and higher (all the 
 other subjects had values between .44 and .61). Do you recommend to redo the 
 analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first value 
 in the .mincost file generated and what does it mean? Can you use this file 
 for other modalities, too? Let's say if I want to do the first level 
 analysis for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value in the aslcal.reg.mincost  file. What is the normal 
 range? Also, I don't understand what you mean with the FSL initialization 
 fails and try --init-spm - can you please give me some more information? 
 Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Try checking the individual registrations (or look at the first value in
 the .mincost file) to find subjects whose registration may have been off
 and so causes the final mask to be non-sense. Sometimes the FSL
 initialization fails. If so, you might try it with --init-spm


 On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

Well, I checked the proper match of ASL and anatomical scans again and one of 
the subjects I reported before was indeed wrongly matched. Thanks! 

What do you mean with So the next thing I would do is to find which subjects 
are the
ones that are off.? You mean off when I check for registration? That's what I 
did before with tkregister2 and they all looked fine to me. What do I look for 
when I open the cbf.talaraich.nii.gz file in fslview? 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, March 12, 2015 12:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

If the registration looks ok, then that is all that counts. However, I'm
a bit sceptical that the reg looks ok but the mincost is that much
different than the others. You should double check that the ASL is
properly matched with the corresponding anatomical (ie, it is not two
different subjects). This would also not explain why the masks were so
far off. So the next thing I would do is to find which subjects are the
ones that are off. You can do this with something like

fslview y.nii.gz

where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
(you can mri_convert it to nii.gz). You can then step through each frame
(or play them as a movie) to see if any look odd.

The mincost is from the BBR cost function. It is basically the mean
gray/white contrast across cortex passed through a sigmoid function to
make its range 0-1, 0 being best. You cannot necessarily generalize the
normal range for one modality to that of another.


On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 I indeed found 3 subjects, whose registration looked ok when I eyeballed them 
 with the tkregister 2 command, with values of .9 and higher (all the other 
 subjects had values between .44 and .61). Do you recommend to redo the 
 analysis without them or to run the first level analysis again with 
 --init-spm instead of --init-fsl in bbregister? Also, how is the first value 
 in the .mincost file generated and what does it mean? Can you use this file 
 for other modalities, too? Let's say if I want to do the first level analysis 
 for fct. connectivity instead of PASL for example?

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 6:34 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 For the range, lower is better, but it impossible to say exactly what is
 good enough because it depends on your data. If it is 0.8 or higher,
 then that is probably bad. What I'm hoping is that there will be one or
 two outliers. The --init-spm was in place of --init-fsl in bbregister.
 But you only need that if you find a bad registration.

 On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value in the aslcal.reg.mincost  file. What is the normal 
 range? Also, I don't understand what you mean with the FSL initialization 
 fails and try --init-spm - can you please give me some more information? 
 Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Try checking the individual registrations (or look at the first value in
 the .mincost file) to find subjects whose registration may have been off
 and so causes the final mask to be non-sense. Sometimes the FSL
 initialization fails. If so, you might try it with --init-spm


 On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I still can't really tell what it is doing. It looks like it is just
 concatenating several input files that are passed on the command line.
 how were those created?


 On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

Oh, I see what you mean. I accidentally sent you the within group analysis 
script. I am attaching the first level analysis script now. I also labeled the 
different steps to simplify the script a little bit. 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11, 2015 4:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

I still can't really tell what it is doing. It looks like it is just
concatenating several input files that are passed on the command line.
how were those created?


On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, the 
 only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

I checked registration before and it was fine. However, I'll go back and look 
at the first value in the aslcal.reg.mincost  file. What is the normal range? 
Also, I don't understand what you mean with the FSL initialization fails and 
try --init-spm - can you please give me some more information? Thanks! 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11, 2015 5:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

Try checking the individual registrations (or look at the first value in
the .mincost file) to find subjects whose registration may have been off
and so causes the final mask to be non-sense. Sometimes the FSL
initialization fails. If so, you might try it with --init-spm


On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I still can't really tell what it is doing. It looks like it is just
 concatenating several input files that are passed on the command line.
 how were those created?


 On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, 
 the only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

Try checking the individual registrations (or look at the first value in 
the .mincost file) to find subjects whose registration may have been off 
and so causes the final mask to be non-sense. Sometimes the FSL 
initialization fails. If so, you might try it with --init-spm


On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I still can't really tell what it is doing. It looks like it is just
 concatenating several input files that are passed on the command line.
 how were those created?


 On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, 
 the only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

This is the script I am using to create cbf.talaraich.mgz (attached).

Thanks,
Rick

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11, 2015 3:22 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

Something went very wrong with your first level analysis because the
final mask is pretty messed up. how did you create cbf.talairach.mgz ?


On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a PASL 
 Regression analysis to subcortical areas only in the tal output file (see 
 below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, the 
 only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


run-pasl_withingroup.sh
Description: run-pasl_withingroup.sh
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
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http://www.partners.org/complianceline . If the e-mail was sent to you in error
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dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

Sure. I simplified it and attached it again. Please let me know if this is 
helpful!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11, 2015 3:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation

Sorry, I don't have time to deconstruct that script. Can you simplify it
for me?

On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, the 
 only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

I still can't really tell what it is doing. It looks like it is just 
concatenating several input files that are passed on the command line. 
how were those created?


On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, the 
 only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 https

Re: [Freesurfer] Monte Carlo Simulation

[Wolthusen, Rick Peter Fritz]

Hi Doug et al.,

Here is the glmdir file you were requesting: 
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


Thanks,
Rick

From: Wolthusen, Rick Peter Fritz
Sent: Tuesday, March 10, 2015 2:10 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: Monte Carlo Simulation

Hi FS Community,

I emailed with Doug a week ago with regards to limiting the results of a PASL 
Regression analysis to subcortical areas only in the tal output file (see 
below). I redid the analysis from scratch adding the flag --mask
$SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to the 
above mentioned mask with regards to the used Mask Vol.. However, the only 
peak I get after the MCS is still in the cortical area. I am more interested in 
the subcortical regions though - what else can I do to limit the results to the 
subcortical regions of interest only?

Thanks,
Rick

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 02, 2015 4:10 PM
To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: Monte Carlo Simulation

Hi Rick, in the future please post to the list and not to us personally.
Thanks! When you did the volume-based analysis, it should have masked
out anything anything that was not subcortical. Did it not? If not, then
when you run mri_glmfit you can add --mask
$SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

doug

On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

Something went very wrong with your first level analysis because the 
final mask is pretty messed up. how did you create cbf.talairach.mgz ?


On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a PASL 
 Regression analysis to subcortical areas only in the tal output file (see 
 below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to 
 the above mentioned mask with regards to the used Mask Vol.. However, the 
 only peak I get after the MCS is still in the cortical area. I am more 
 interested in the subcortical regions though - what else can I do to limit 
 the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the
 cortical area but not in sub-cortical areas (the cortical clusters
 where consistent with the clusters I found in the cortical analyses
 though). Is there a way I can limit the Monte Carlo Simulation to
 sub-cortical areas only so that I'll also see the most sgn. clusters
 in the sub-cortical areas? Please let me know if you have any
 additional questions!

 Thanks,
 Rick
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

For the range, lower is better, but it impossible to say exactly what is 
good enough because it depends on your data. If it is 0.8 or higher, 
then that is probably bad. What I'm hoping is that there will be one or 
two outliers. The --init-spm was in place of --init-fsl in bbregister. 
But you only need that if you find a bad registration.

On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and look 
 at the first value in the aslcal.reg.mincost  file. What is the normal range? 
 Also, I don't understand what you mean with the FSL initialization fails 
 and try --init-spm - can you please give me some more information? Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Try checking the individual registrations (or look at the first value in
 the .mincost file) to find subjects whose registration may have been off
 and so causes the final mask to be non-sense. Sometimes the FSL
 initialization fails. If so, you might try it with --init-spm


 On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote:
 Oh, I see what you mean. I accidentally sent you the within group analysis 
 script. I am attaching the first level analysis script now. I also labeled 
 the different steps to simplify the script a little bit.
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 4:50 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 I still can't really tell what it is doing. It looks like it is just
 concatenating several input files that are passed on the command line.
 how were those created?


 On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote:
 Sure. I simplified it and attached it again. Please let me know if this is 
 helpful!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:36 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Sorry, I don't have time to deconstruct that script. Can you simplify it
 for me?

 On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
 This is the script I am using to create cbf.talaraich.mgz (attached).

 Thanks,
 Rick
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, March 11, 2015 3:22 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Simulation

 Something went very wrong with your first level analysis because the
 final mask is pretty messed up. how did you create cbf.talairach.mgz ?


 On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug et al.,

 Here is the glmdir file you were requesting: 
 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928


 Thanks,
 Rick
 
 From: Wolthusen, Rick Peter Fritz
 Sent: Tuesday, March 10, 2015 2:10 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Subject: RE: Monte Carlo Simulation

 Hi FS Community,

 I emailed with Doug a week ago with regards to limiting the results of a 
 PASL Regression analysis to subcortical areas only in the tal output file 
 (see below). I redid the analysis from scratch adding the flag --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the 
 Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers 
 to the above mentioned mask with regards to the used Mask Vol.. 
 However, the only peak I get after the MCS is still in the cortical area. 
 I am more interested in the subcortical regions though - what else can I 
 do to limit the results to the subcortical regions of interest only?

 Thanks,
 Rick
 
 From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, March 02, 2015 4:10 PM
 To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: Monte Carlo Simulation

 Hi Rick, in the future please post to the list and not to us personally.
 Thanks! When you did the volume-based analysis, it should have masked
 out anything anything that was not subcortical. Did it not? If not, then
 when you run mri_glmfit you can add --mask
 $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the 
 trick.

 doug

 On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

mris_preproc might work. You could also use mri_concat (mris_preproc is 
a front end for mri_concat)

On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote:

 Am 03.03.2015 um 14:42 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 Some of this Martin will have to comment on, but my comments below

 On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
 Hey Doug,

 thanks again! That means, I would do something like:

 1.) construct longitudinal qdec table
 - only use fsid, fsid-base, and years/age columns
 - substract the average age of the one-time point subjects from years/age 
 value for every subject at every time point

 2.) run long_mris_slopes
 - use the --do-avg flag?
 Yes, I think so
 3.) concatenate the output files from 2) and the maps from the one-time 
 point subjects with mris_preproc
 - use --is flag to select maps by specifying full path
 What command are you talking about to do the concatenation?
 mris_preproc, I thought.

 Thanks for your help,

 Janosch

 Otherwise sounds right. Make sure you use the average of the time points 
 from long_mris_slopes and not the slope.
 4.) run mri_glmfit
 - use --osgm flag for one-sample group mean
 Yes
 5.) replace sig.mgz file with the one from LME analysis and run 
 mri_glmfit-sim
 Yes
 Is that correct? (especially, is using --do-avg what you meant by taking 
 the offset)

 Thanks,

 Janosch


 Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 I don't know, esp since it is an approximation to begin with. An 
 alternative is to take the offsets from your multi-time-point subjects and 
 the single maps from your subjects with one time point and run that 
 through the one-sample-group-mean (--osgm in mri_glmfit). If you go this 
 route, then you should subtract the mean age of the one time-point 
 subjects from the age of the multi-time point subjects before the 1st 
 stage of analysis.

 doug


 On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
 Hi Doug,

 thank you very much for your answer!

 Am 02.03.2015 um 11:30 schrieb Douglas N Greve 
 gr...@nmr.mgh.harvard.edu:

 You would do the long analysis using a random effects analysis.
 OK, so basically do 2-stage modeling 
 (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), 
 right?

 For each subject you can get a slope (this won't work if the subject 
 only has 1 time point), then concatenate the slopes into a file and run 
 mri_glmfit, then follow the procedures from the archive email you 
 reference.
 One quarter of my subjects only has one measurement time point. Can I 
 still use this method (which would only consider the 3/4 of the subjects) 
 to correct clusters found in the whole group? Or would it only be valid 
 for correcting clusters from an LME model for the reduced group?

 Thanks,

 Janosch

 doug

 On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,

 I would like apply (Monte Carlo simulation) cluster correction (as 
 opposed to the implemented vertex-wise FDR correction) on the results 
 from a longitudinal study I analyzed using the LME toolbox. The design 
 is unbalanced (different number of time points, from 1 to 4, per 
 subject).

 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
  you, Doug, suggested, if I understand correctly:

 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with 
 time) as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`

 How would I extend this to my case where I don't have pairwise images, 
 but 1 image for some participants, for others up to 4?

 Thanks a lot,

 Janosch




 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the person to whom 
 it is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you 
 in error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.

 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

I don't know, esp since it is an approximation to begin with. An 
alternative is to take the offsets from your multi-time-point subjects 
and the single maps from your subjects with one time point and run that 
through the one-sample-group-mean (--osgm in mri_glmfit). If you go this 
route, then you should subtract the mean age of the one time-point 
subjects from the age of the multi-time point subjects before the 1st 
stage of analysis.

doug


On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
 Hi Doug,

 thank you very much for your answer!

 Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 You would do the long analysis using a random effects analysis.
 OK, so basically do 2-stage modeling 
 (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right?

 For each subject you can get a slope (this won't work if the subject only 
 has 1 time point), then concatenate the slopes into a file and run 
 mri_glmfit, then follow the procedures from the archive email you reference.
 One quarter of my subjects only has one measurement time point. Can I still 
 use this method (which would only consider the 3/4 of the subjects) to 
 correct clusters found in the whole group? Or would it only be valid for 
 correcting clusters from an LME model for the reduced group?

 Thanks,

 Janosch

 doug

 On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,

 I would like apply (Monte Carlo simulation) cluster correction (as opposed 
 to the implemented vertex-wise FDR correction) on the results from a 
 longitudinal study I analyzed using the LME toolbox. The design is 
 unbalanced (different number of time points, from 1 to 4, per subject).

 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
  you, Doug, suggested, if I understand correctly:

 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with time) 
 as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`

 How would I extend this to my case where I don't have pairwise images, but 
 1 image for some participants, for others up to 4?

 Thanks a lot,

 Janosch




 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.




-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Janosch Linkersdörfer]

Am 03.03.2015 um 14:42 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 
 Some of this Martin will have to comment on, but my comments below
 
 On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
 Hey Doug,
 
 thanks again! That means, I would do something like:
 
 1.) construct longitudinal qdec table
 - only use fsid, fsid-base, and years/age columns
 - substract the average age of the one-time point subjects from years/age 
 value for every subject at every time point
 
 2.) run long_mris_slopes
 - use the --do-avg flag?
 Yes, I think so
 
 3.) concatenate the output files from 2) and the maps from the one-time 
 point subjects with mris_preproc
 - use --is flag to select maps by specifying full path
 What command are you talking about to do the concatenation?

mris_preproc, I thought.

Thanks for your help,

Janosch

 Otherwise sounds right. Make sure you use the average of the time points from 
 long_mris_slopes and not the slope.
 
 4.) run mri_glmfit
 - use --osgm flag for one-sample group mean
 Yes
 
 5.) replace sig.mgz file with the one from LME analysis and run 
 mri_glmfit-sim
 Yes
 
 Is that correct? (especially, is using --do-avg what you meant by taking the 
 offset)
 
 Thanks,
 
 Janosch
 
 
 Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:
 
 I don't know, esp since it is an approximation to begin with. An 
 alternative is to take the offsets from your multi-time-point subjects and 
 the single maps from your subjects with one time point and run that through 
 the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, 
 then you should subtract the mean age of the one time-point subjects from 
 the age of the multi-time point subjects before the 1st stage of analysis.
 
 doug
 
 
 On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
 Hi Doug,
 
 thank you very much for your answer!
 
 Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:
 
 You would do the long analysis using a random effects analysis.
 OK, so basically do 2-stage modeling 
 (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), 
 right?
 
 For each subject you can get a slope (this won't work if the subject only 
 has 1 time point), then concatenate the slopes into a file and run 
 mri_glmfit, then follow the procedures from the archive email you 
 reference.
 One quarter of my subjects only has one measurement time point. Can I 
 still use this method (which would only consider the 3/4 of the subjects) 
 to correct clusters found in the whole group? Or would it only be valid 
 for correcting clusters from an LME model for the reduced group?
 
 Thanks,
 
 Janosch
 
 doug
 
 On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,
 
 I would like apply (Monte Carlo simulation) cluster correction (as 
 opposed to the implemented vertex-wise FDR correction) on the results 
 from a longitudinal study I analyzed using the LME toolbox. The design 
 is unbalanced (different number of time points, from 1 to 4, per 
 subject).
 
 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
  you, Doug, suggested, if I understand correctly:
 
 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with 
 time) as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`
 
 How would I extend this to my case where I don't have pairwise images, 
 but 1 image for some participants, for others up to 4?
 
 Thanks a lot,
 
 Janosch
 
 
 
 
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
 
 
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
 
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

Some of this Martin will have to comment on, but my comments below

On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
 Hey Doug,

 thanks again! That means, I would do something like:

 1.) construct longitudinal qdec table
 - only use fsid, fsid-base, and years/age columns
 - substract the average age of the one-time point subjects from years/age 
 value for every subject at every time point

 2.) run long_mris_slopes
 - use the --do-avg flag?
Yes, I think so

 3.) concatenate the output files from 2) and the maps from the one-time point 
 subjects with mris_preproc
 - use --is flag to select maps by specifying full path
What command are you talking about to do the concatenation? Otherwise 
sounds right. Make sure you use the average of the time points from 
long_mris_slopes and not the slope.

 4.) run mri_glmfit
 - use --osgm flag for one-sample group mean
Yes

 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim
Yes

 Is that correct? (especially, is using --do-avg what you meant by taking the 
 offset)

 Thanks,

 Janosch


 Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 I don't know, esp since it is an approximation to begin with. An alternative 
 is to take the offsets from your multi-time-point subjects and the single 
 maps from your subjects with one time point and run that through the 
 one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you 
 should subtract the mean age of the one time-point subjects from the age of 
 the multi-time point subjects before the 1st stage of analysis.

 doug


 On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
 Hi Doug,

 thank you very much for your answer!

 Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 You would do the long analysis using a random effects analysis.
 OK, so basically do 2-stage modeling 
 (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), 
 right?

 For each subject you can get a slope (this won't work if the subject only 
 has 1 time point), then concatenate the slopes into a file and run 
 mri_glmfit, then follow the procedures from the archive email you 
 reference.
 One quarter of my subjects only has one measurement time point. Can I still 
 use this method (which would only consider the 3/4 of the subjects) to 
 correct clusters found in the whole group? Or would it only be valid for 
 correcting clusters from an LME model for the reduced group?

 Thanks,

 Janosch

 doug

 On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,

 I would like apply (Monte Carlo simulation) cluster correction (as 
 opposed to the implemented vertex-wise FDR correction) on the results 
 from a longitudinal study I analyzed using the LME toolbox. The design is 
 unbalanced (different number of time points, from 1 to 4, per subject).

 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
  you, Doug, suggested, if I understand correctly:

 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with 
 time) as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`

 How would I extend this to my case where I don't have pairwise images, 
 but 1 image for some participants, for others up to 4?

 Thanks a lot,

 Janosch




 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Janosch Linkersdörfer]

Hey Doug,

thanks again! That means, I would do something like:

1.) construct longitudinal qdec table
- only use fsid, fsid-base, and years/age columns
- substract the average age of the one-time point subjects from years/age value 
for every subject at every time point

2.) run long_mris_slopes
- use the --do-avg flag?

3.) concatenate the output files from 2) and the maps from the one-time point 
subjects with mris_preproc
- use --is flag to select maps by specifying full path

4.) run mri_glmfit
- use --osgm flag for one-sample group mean

5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim

Is that correct? (especially, is using --do-avg what you meant by taking the 
offset)

Thanks,

Janosch


Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 
 I don't know, esp since it is an approximation to begin with. An alternative 
 is to take the offsets from your multi-time-point subjects and the single 
 maps from your subjects with one time point and run that through the 
 one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you 
 should subtract the mean age of the one time-point subjects from the age of 
 the multi-time point subjects before the 1st stage of analysis.
 
 doug
 
 
 On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
 Hi Doug,
 
 thank you very much for your answer!
 
 Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:
 
 You would do the long analysis using a random effects analysis.
 OK, so basically do 2-stage modeling 
 (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right?
 
 For each subject you can get a slope (this won't work if the subject only 
 has 1 time point), then concatenate the slopes into a file and run 
 mri_glmfit, then follow the procedures from the archive email you reference.
 One quarter of my subjects only has one measurement time point. Can I still 
 use this method (which would only consider the 3/4 of the subjects) to 
 correct clusters found in the whole group? Or would it only be valid for 
 correcting clusters from an LME model for the reduced group?
 
 Thanks,
 
 Janosch
 
 doug
 
 On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,
 
 I would like apply (Monte Carlo simulation) cluster correction (as opposed 
 to the implemented vertex-wise FDR correction) on the results from a 
 longitudinal study I analyzed using the LME toolbox. The design is 
 unbalanced (different number of time points, from 1 to 4, per subject).
 
 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
  you, Doug, suggested, if I understand correctly:
 
 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with 
 time) as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`
 
 How would I extend this to my case where I don't have pairwise images, but 
 1 image for some participants, for others up to 4?
 
 Thanks a lot,
 
 Janosch
 
 
 
 
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
 
 
 
 
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 


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Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

Hi Rick, in the future please post to the list and not to us personally. 
Thanks! When you did the volume-based analysis, it should have masked 
out anything anything that was not subcortical. Did it not? If not, then 
when you run mri_glmfit you can add --mask 
$SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

doug

On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
 Hi Doug,

 I was running the following command in launchpad in order to correct 
 for multiple comparison (using a output file from a PASL FS analysis):

 pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir 
 tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0 
 cbf.talairach_p01_abs_montecarlo


 When I looked for the surviving clusters, I just found clusters in the 
 cortical area but not in sub-cortical areas (the cortical clusters 
 where consistent with the clusters I found in the cortical analyses 
 though). Is there a way I can limit the Monte Carlo Simulation to 
 sub-cortical areas only so that I'll also see the most sgn. clusters 
 in the sub-cortical areas? Please let me know if you have any 
 additional questions!

 Thanks,
 Rick

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Janosch Linkersdörfer]

Hi Doug,

thank you very much for your answer!

Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu:

 
 You would do the long analysis using a random effects analysis.

OK, so basically do 2-stage modeling 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right?

 For each subject you can get a slope (this won't work if the subject only has 
 1 time point), then concatenate the slopes into a file and run mri_glmfit, 
 then follow the procedures from the archive email you reference.

One quarter of my subjects only has one measurement time point. Can I still use 
this method (which would only consider the 3/4 of the subjects) to correct 
clusters found in the whole group? Or would it only be valid for correcting 
clusters from an LME model for the reduced group?

Thanks,

Janosch

 doug
 
 On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,
 
 I would like apply (Monte Carlo simulation) cluster correction (as opposed 
 to the implemented vertex-wise FDR correction) on the results from a 
 longitudinal study I analyzed using the LME toolbox. The design is 
 unbalanced (different number of time points, from 1 to 4, per subject).
 
 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) 
 you, Doug, suggested, if I understand correctly:
 
 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with time) 
 as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`
 
 How would I extend this to my case where I don't have pairwise images, but 1 
 image for some participants, for others up to 4?
 
 Thanks a lot,
 
 Janosch
 
 
 
 
 
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

You would do the long analysis using a random effects analysis. For each 
subject you can get a slope (this won't work if the subject only has 1 
time point), then concatenate the slopes into a file and run mri_glmfit, 
then follow the procedures from the archive email you reference.
doug

On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
 Hi Doug and others,

 I would like apply (Monte Carlo simulation) cluster correction (as opposed to 
 the implemented vertex-wise FDR correction) on the results from a 
 longitudinal study I analyzed using the LME toolbox. The design is unbalanced 
 (different number of time points, from 1 to 4, per subject).

 In this thread 
 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) 
 you, Doug, suggested, if I understand correctly:

 - concatenating the images using `mris_preproc --paired-diff`
 - smooth with the same kernel size as used in the lme analysis
 - running `mri_glmfit` on them with an fsgd file that uses the same 
 covariates and the same contrast (excluding the interaction term with time) 
 as used in the lme analysis
 - overwriting sig.mgh with the one from the lme analysis
 - running `mri_glmfit-sim --cache`

 How would I extend this to my case where I don't have pairwise images, but 1 
 image for some participants, for others up to 4?

 Thanks a lot,

 Janosch





-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Janosch Linkersdörfer]

Hi Doug and others,

I would like apply (Monte Carlo simulation) cluster correction (as opposed to 
the implemented vertex-wise FDR correction) on the results from a longitudinal 
study I analyzed using the LME toolbox. The design is unbalanced (different 
number of time points, from 1 to 4, per subject).

In this thread 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) 
you, Doug, suggested, if I understand correctly:

- concatenating the images using `mris_preproc --paired-diff`
- smooth with the same kernel size as used in the lme analysis
- running `mri_glmfit` on them with an fsgd file that uses the same covariates 
and the same contrast (excluding the interaction term with time) as used in the 
lme analysis
- overwriting sig.mgh with the one from the lme analysis
- running `mri_glmfit-sim --cache`

How would I extend this to my case where I don't have pairwise images, but 1 
image for some participants, for others up to 4?

Thanks a lot,

Janosch



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Hi Doug, 

I tested this new script on volume data and it did create the file 
'sig.masked.mgh', which shows the significance map masked by Monte Carlo 
surviving clusters. So, I guess you can update the current file now. 

Thanks!
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 11, 2014 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

I think it must have gotten contaminated as an attachement. Try using
this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 
 'Permissions' tab of this file, 'Allow executing file as program' option is 
 checked.

 I can try cd'ing into that folder then run the command as :

 mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3 mcz1_1.3 
 --sim-sign abs --cwpvalthresh .05
 but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
 the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.

 Hamdi



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, September 10, 2014 4:10 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Not sure what is wrong. Is it executable? Were you able to save the file
 from your email or did you cut and paste it into a file and save the file?


 On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Running it as you suggested didn't work either. I tried it as follows:

 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 
 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

 It says:

 'nknown option: `-
 Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

 Then I thought maybe this is a c shell script so I need to use ./ before the 
 command. I tried that but it gave the same error as above.

 Any ideas?

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 6:14 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Yes, you can just run

 /path/to/your/local/copy/mri_glmfit-sim



 On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I 
 can run this new 'mri_glmfit-sim' you sent me? The original 
 'mri_glmfit-sim' that I use is under 
 '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

great, I'll check it in to the source so it will be part of the next version
thanks
doug
On 09/12/2014 10:31 AM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I tested this new script on volume data and it did create the file 
 'sig.masked.mgh', which shows the significance map masked by Monte Carlo 
 surviving clusters. So, I guess you can update the current file now.

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Thursday, September 11, 2014 1:55 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 I think it must have gotten contaminated as an attachement. Try using
 this one

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


 On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Yes I could save the file from my email into '/homes/8/hhe0/Documents'. 
 Under 'Permissions' tab of this file, 'Allow executing file as program' 
 option is checked.

 I can try cd'ing into that folder then run the command as :

 mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3 mcz1_1.3 
 --sim-sign abs --cwpvalthresh .05
 but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
 the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.

 Hamdi



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, September 10, 2014 4:10 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Not sure what is wrong. Is it executable? Were you able to save the file
 from your email or did you cut and paste it into a file and save the file?


 On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Running it as you suggested didn't work either. I tried it as follows:

 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim 
 mc-z 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

 It says:

 'nknown option: `-
 Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

 Then I thought maybe this is a c shell script so I need to use ./ before 
 the command. I tried that but it gave the same error as above.

 Any ideas?

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 6:14 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Yes, you can just run

 /path/to/your/local/copy/mri_glmfit-sim



 On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I 
 can run this new 'mri_glmfit-sim' you sent me? The original 
 'mri_glmfit-sim' that I use is under 
 '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

I think it must have gotten contaminated as an attachement. Try using 
this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 
 'Permissions' tab of this file, 'Allow executing file as program' option is 
 checked.

 I can try cd'ing into that folder then run the command as :

 mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3 mcz1_1.3 
 --sim-sign abs --cwpvalthresh .05
 but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
 the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.

 Hamdi



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, September 10, 2014 4:10 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Not sure what is wrong. Is it executable? Were you able to save the file
 from your email or did you cut and paste it into a file and save the file?


 On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Running it as you suggested didn't work either. I tried it as follows:

 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 
 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

 It says:

 'nknown option: `-
 Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

 Then I thought maybe this is a c shell script so I need to use ./ before the 
 command. I tried that but it gave the same error as above.

 Any ideas?

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 6:14 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Yes, you can just run

 /path/to/your/local/copy/mri_glmfit-sim



 On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I 
 can run this new 'mri_glmfit-sim' you sent me? The original 
 'mri_glmfit-sim' that I use is under 
 '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Thanks Doug! It seems to be working this time. I will keep you posted on the 
results. 

Best,
Hamdi




From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 11, 2014 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

I think it must have gotten contaminated as an attachement. Try using
this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 
 'Permissions' tab of this file, 'Allow executing file as program' option is 
 checked.

 I can try cd'ing into that folder then run the command as :

 mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3 mcz1_1.3 
 --sim-sign abs --cwpvalthresh .05
 but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
 the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.

 Hamdi



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, September 10, 2014 4:10 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Not sure what is wrong. Is it executable? Were you able to save the file
 from your email or did you cut and paste it into a file and save the file?


 On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Running it as you suggested didn't work either. I tried it as follows:

 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 
 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

 It says:

 'nknown option: `-
 Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

 Then I thought maybe this is a c shell script so I need to use ./ before the 
 command. I tried that but it gave the same error as above.

 Any ideas?

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 6:14 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Yes, you can just run

 /path/to/your/local/copy/mri_glmfit-sim



 On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I 
 can run this new 'mri_glmfit-sim' you sent me? The original 
 'mri_glmfit-sim' that I use is under 
 '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Hi Doug,

Running it as you suggested didn't work either. I tried it as follows:

1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 
1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

It says:

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

Then I thought maybe this is a c shell script so I need to use ./ before the 
command. I tried that but it gave the same error as above.

Any ideas?

Thanks!
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 09, 2014 6:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Yes, you can just run

/path/to/your/local/copy/mri_glmfit-sim



On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. So 
 I can't really copy it over. Is it possible to run this locally? I'm working 
 on a linux workstation at Martinos and when I ask the source, it gives me 
 that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I can 
 run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' 
 that I use is under '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

Not sure what is wrong. Is it executable? Were you able to save the file 
from your email or did you cut and paste it into a file and save the file?


On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Running it as you suggested didn't work either. I tried it as follows:

 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 
 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

 It says:

 'nknown option: `-
 Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

 Then I thought maybe this is a c shell script so I need to use ./ before the 
 command. I tried that but it gave the same error as above.

 Any ideas?

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 6:14 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Yes, you can just run

 /path/to/your/local/copy/mri_glmfit-sim



 On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I can 
 run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' 
 that I use is under '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 
'Permissions' tab of this file, 'Allow executing file as program' option is 
checked. 

I can try cd'ing into that folder then run the command as :

 mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3 mcz1_1.3 
 --sim-sign abs --cwpvalthresh .05

but I'm not sure if it will then use the new mri_glmfit-sim file you sent or 
the original file under '/usr/local/freesurfer/stable5_0_0/bin/'.  

Hamdi




From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 10, 2014 4:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Not sure what is wrong. Is it executable? Were you able to save the file
from your email or did you cut and paste it into a file and save the file?


On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Running it as you suggested didn't work either. I tried it as follows:

 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 
 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05

 It says:

 'nknown option: `-
 Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

 Then I thought maybe this is a c shell script so I need to use ./ before the 
 command. I tried that but it gave the same error as above.

 Any ideas?

 Thanks!
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 6:14 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 Yes, you can just run

 /path/to/your/local/copy/mri_glmfit-sim



 On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. 
 So I can't really copy it over. Is it possible to run this locally? I'm 
 working on a linux workstation at Martinos and when I ask the source, it 
 gives me that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I can 
 run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' 
 that I use is under '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Hi Doug, 

Thanks for your reply. I can certainly test it. Could you tell me how I can run 
this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use 
is under '/usr/local/freesurfer/stable5_0_0/bin/'

Best,
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, September 08, 2014 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

That was an oversight. I've attached a version that should work. Can you
test it for me? Once I know it works I'll check it in to tree.
doug




On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

You can just copy it over the old one (but make  a backup of it first)

On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I can 
 run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that 
 I use is under '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Hi Doug, 

I don't seem to have the permission to change the contents of that folder. So I 
can't really copy it over. Is it possible to run this locally? I'm working on a 
linux workstation at Martinos and when I ask the source, it gives me that 
folder: 

which mri_glmfit-sim
/usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim




From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 09, 2014 5:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

You can just copy it over the old one (but make  a backup of it first)

On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I can 
 run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that 
 I use is under '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

Yes, you can just run

/path/to/your/local/copy/mri_glmfit-sim



On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 I don't seem to have the permission to change the contents of that folder. So 
 I can't really copy it over. Is it possible to run this locally? I'm working 
 on a linux workstation at Martinos and when I ask the source, it gives me 
 that folder:

 which mri_glmfit-sim
 /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim



 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 09, 2014 5:24 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 You can just copy it over the old one (but make  a backup of it first)

 On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
 Hi Doug,

 Thanks for your reply. I can certainly test it. Could you tell me how I can 
 run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' 
 that I use is under '/usr/local/freesurfer/stable5_0_0/bin/'

 Best,
 Hamdi


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Monday, September 08, 2014 11:48 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

 That was an oversight. I've attached a version that should work. Can you
 test it for me? Once I know it works I'll check it in to tree.
 doug




 On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
 Dear FS experts,

 I have a question about a MC output file. When I run the MC sim
 (using mri_glmfit-sim) on the surface, it generates a bunch of files
 including a 'sig.masked.mgh', which is nice for displaying the
 significance map limited to the clusters that survive the MC
 correction. However, when I run it on the volume, it doesn't generate
 this specific file. Does anyone know the reason for that? Is there an
 alternative way to display the significance map that show only the
 clusters that survive the MC correction?

 Many thanks!
 Hamdi


 --

 Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Psychiatric Neuroimaging Division
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462
 Email:heryil...@partners.org mailto:heryil...@partners.org


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Douglas N Greve]

That was an oversight. I've attached a version that should work. Can you 
test it for me? Once I know it works I'll check it in to tree.

doug




On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:

Dear FS experts,

I have a question about a MC output file. When I run the MC sim 
(using mri_glmfit-sim) on the surface, it generates a bunch of files 
including a 'sig.masked.mgh', which is nice for displaying the 
significance map limited to the clusters that survive the MC 
correction. However, when I run it on the volume, it doesn't generate 
this specific file. Does anyone know the reason for that? Is there an 
alternative way to display the significance map that show only the 
clusters that survive the MC correction?


Many thanks!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email:heryil...@partners.org mailto:heryil...@partners.org


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

#!/bin/tcsh -f
set VERSION = '$Id: mri_glmfit-sim,v 1.36.2.6 2013/06/05 17:06:31 greve Exp $';

set inputargs = ($argv);

set glmdir = ()
set nulltype = ();
set nsim = ()
set thresh = ()
set csdbase = ()
set simsign = ()
set cwpvalthresh = .05
set Overwrite = 0;
set DoSim = 1;
set LF = ();
set AllDoneFile = ();
set Seed = ();
set fwhmOverride = ();
set UseUniformPDF = 0;
set UniformPDFMin = ();
set UniformPDFMax = ();
set DiagCluster = 0;
set PBNodeType = ();
set UseCache = 0;
set PermForce = 0;
set UseGRF = 0;
set volsubject = fsaverage;
set subjectOverride = ();
set Bonferroni = 0;
set ReportCentroid = 0;
set annot = aparc

set nJobs = 1;
set DoBackground = 0;
set DoPBSubmit = 0;
set DoPoll = 0;
set tSleepSec = 10;

set CacheDir = $FREESURFER_HOME/average/mult-comp-cor
set CacheLabel = cortex;

set tmpdir = ();
set CleanUp = 1;
set PrintHelp = 0;

if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e --help | wc -l` 
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
endif
set n = `echo $argv | grep -e --version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif

goto parse_args;
parse_args_return:

goto check_params;
check_params_return:

if(! -e $glmdir) then
  echo ERROR: cannot find $glmdir
  exit 1;
endif

set glmfitlog = $glmdir/mri_glmfit.log
if(! -e $glmfitlog) then
  echo ERROR: cannot find $glmfitlog
  exit 1;
endif

set mask = `stem2fname $glmdir/mask`
if($status) then
  echo $mask
  exit 1;
endif

if($nulltype != perm) then
  set fwhmfile = $glmdir/fwhm.dat
  if(! -e $fwhmfile) then
echo ERROR: cannot find $fwhm
exit 1;
  endif
  # This may be overridden
  set fwhm = `cat $fwhmfile`;
else
  set fwhm = 0;
endif

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == cwd) print $2}'`
if(! -e $glmfitcwd) then
  echo ERROR: cannot find $glmfitcwd
  exit 1;
endif

set anattype = volume;
set subject = ();
set hemi = ();
set surf = white;
set y = ();
set wls = ();

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == cwd) print $2}'`

# Go through the original mri_glmfit command-line
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == cmdline) print $0}'`
set glmfitcmd = ($glmfitcmd0);
echo $glmfitcmd
set gd2mtx = dods
set label = ();
while($#glmfitcmd)
  set flag = $glmfitcmd[1]; shift glmfitcmd;
  #echo $flag
  switch($flag)
  case --surf
  case --surface
set subject = $glmfitcmd[1]; shift glmfitcmd;
set hemi= $glmfitcmd[1]; shift glmfitcmd;
set anattype = surface;
if($#glmfitcmd != 0) then
  set c = `echo $glmfitcmd[1] | cut -c 1-2`;
  if($c != --) then
set surf = $glmfitcmd[1]; shift glmfitcmd;
  endif
endif
breaksw
  case --fsgd
shift glmfitcmd;
if($#glmfitcmd  0) then
  if($glmfitcmd[1] == doss) set gd2mtx = doss
endif
breaksw
  case --label
set label = $glmfitcmd[1]; shift glmfitcmd;
breaksw
  case --perm-force
# Probably never gets here
set PermForce = 1;
breaksw
  case --y
set y = $glmfitcwd/$glmfitcmd[1]; shift glmfitcmd;
if(! -e $y) then
  set y = $glmdir/`basename $y`
  if(! -e $y) then
echo ERROR: cannot find $y
exit 1;
  endif
endif
breaksw
  case --wls
set wls = $glmfitcwd/$glmfitcmd[1]; shift glmfitcmd;
if(! -e $wls) then
  set wls = $glmdir/`basename $wls`
  if(! -e $wls) then
echo ERROR: cannot find $wls
exit 1;
  endif
endif
breaksw
  # Ignore these options that have no args
  case cmdline
  

[Freesurfer] Monte Carlo Sim output / sig.masked.mgh

[Eryilmaz, Huseyin Hamdi]

Dear FS experts,

I have a question about a MC output file. When I run the MC sim (using 
mri_glmfit-sim) on the surface, it generates a bunch of files including a 
'sig.masked.mgh', which is nice for displaying the significance map limited to 
the clusters that survive the MC correction. However, when I run it on the 
volume, it doesn't generate this specific file. Does anyone know the reason for 
that? Is there an alternative way to display the significance map that show 
only the clusters that survive the MC correction?

Many thanks!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email: heryil...@partners.orgmailto:heryil...@partners.org
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[Freesurfer] Monte Carlo correction

[Johnson, Eileanoir]

Hi there,

I am trying to run a monte carlo correction on my average subject, using the 
full mri-mcsim run with 1 iterations (and about 200 participants). This is 
taking a long time, and the cluster I have access to has a limit of 72 hours 
which isn't long enough to finish processing. Is there a way to cut down on 
this processing time, i.e. cutting down on the iterations etc?

Many thanks,
Eileanoir


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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Monte Carlo Cluster Size Threshold

[Wegman, Clem J.]

Hello Freesurfer Experts,

I am looking for the threshold cluster size used in a Monte Carlo Simulation 
(ran in qdec) at p=0.05. I believe the attached pdf (used to be 
mc-z.abs.th13.pdf) contains this information but I am not sure about how it is 
annotated. Does MaxClustBin correspond to a cluster size (in mm^2) and 
MaxClustPDF correspond to the p-value? From this file p=0.05 would correspond 
to a cluster size of 375.6 mm^2. I am basing these assumptions off of a 
previous message from the archives 
(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-August/032738.html),
 although I am looking at a different file because the one suggested 
(cache.th13.abs.pdf.dat) did not seem to contain the correct information. 
Thanks a bunch for your help!

-John
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Re: [Freesurfer] Monte Carlo Cluster Size Threshold

[Wegman, Clem J.]

Just realized I didn't attach the pdf in the initial email. Sorry!


On May 20, 2014, at 12:01 PM, Wegman, Clem J. wrote:

 Hello Freesurfer Experts,

 I am looking for the threshold cluster size used in a Monte Carlo Simulation 
 (ran in qdec) at p=0.05. I believe the attached pdf (used to be 
 mc-z.abs.th13.pdf) contains this information but I am not sure about how it 
 is annotated. Does MaxClustBin correspond to a cluster size (in mm^2) and 
 MaxClustPDF correspond to the p-value? From this file p=0.05 would 
 correspond to a cluster size of 375.6 mm^2. I am basing these assumptions off 
 of a previous message from the archives 
 (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-August/032738.html),
  although I am looking at a different file because the one suggested 
 (cache.th13.abs.pdf.dat) did not seem to contain the correct information. 
 Thanks a bunch for your help!

 -John
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 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.




mc-z.abs.th13.pdf
Description: mc-z.abs.th13.pdf
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Pedro Rosa]

Thanks, Doug!
I looked at the examples on the wiki, and the Paired Analysis wiki page as well.
You mentioned I should include the categorical and continuous variables in the 
fsgd file for the mri_glmfit. It seems that one of my analyses includes few 
subjects,  and then one of the class end up lacking a adequate range of 
continuous variables, and consequently the mri_glmfit finished with errors 
(this error no longer appears after I merged that problematic group with 
another).
Therefore I ask whether it would be fine to run the mri_glmfit without some (or 
all) the continuous  or/an categorical variables, while they would of course be 
included in the LME ran in MatLab.
Further, I would like to ask what the FMHM outputs represents?
Regards,
Pedro Rosa.


On Wednesday, April 16, 2014 at 11:49 AM, Douglas N Greve wrote:

  
 On 04/15/2014 10:34 PM, Pedro Rosa wrote:
  Hi, Doug.
  Thanks a lot!
  The command would look like this: mri_glmfit-sim --glmdir  
  lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs  
  --overwrite --cache 1.3 abs
  It takes only a few seconds to run.
   
  
 The command is fine, but remove --sim mc-z 1 2 teste. This tells it  
 to do the simulation, which you don't need to do. It is overridden by  
 the --cache flag. If they had occurred in the other order, you would be  
 waiting days for the simulation to run.
  I have a few questions about how to run it:
  1) How the single entry for each subject look like in the FSGD file?
   
  
 I'm not sure what you mean. Have you looked at the examples on the wiki?
   
  2) How to define the voxel/vertex-wise used to define clusters (after  
  —sim, -log10( p)), and the voxel-wise threshold for the —cache option?
  What is the difference between them?
   
  
 They are the same
 doug
   
  Thanks again,
  Pedro Rosa.
   
  On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote:
   

   On 04/14/2014 10:35 AM, Pedro Rosa wrote:
Dear Doug and Jorge,
I tried what you suggested and I think it work, although I have some
concerns.
I am working with a longitudinal study with two time-points for all
subjects, three categorical variables (group, substance abuse /
dependence and gender) and three continuous variables (interval
between scans, age and medication intake).
I generated a contrast with intercept + 7 betas for the LME, ran it
without any problem and saved the sig.mgh using
fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’).
For the mri_glmfit I entered the same output from mri_surf2surf I used
for the LME (smoothed at 10mm), but I did not know how exactly to
enter the categorical and continuous variables, or which contrast to  
use.
 

   I would do it as a paired-test (see the wiki). You may have to re-run
   mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this
   as the input to mri_glmfit. Set up the FSGD with the categorical and
   continuous variables (note that the FSGD file will have only a single
   entry per subject). Create your contrasts and run mri_glmfit. Overwrite
   the sig.mgh with the one from LME. Then run mri_glmfit-sim with the
   --cache option (not permutation)

   I don't know what your contrast of interest is, so I can't help you
   there. In the end, it does not matter because you are overwriting the
   sig map anyway. You just need a contrast as a place holder.

   doug

The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch
 
I just tested creating a matrix with 24 columns
(Nclasses*(Nvariables+1) as suggested for DODS).
Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir
Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished
apparently without errors.
I attached the logs for both mri_glmfit and mri_glmfit-sim.
 
That said, I have the following questions:
 
1) What does the FWHM procedure does?
2) How should I decide which contrast to test if the mri_glmfit does
not consider the longitudinal design?
3) Will the mri_glmfit-sim consider only the FMHM output from
mri_glmfit and sig.mgh from the LME, or also other outputs from the
mri_glmfit?
4) Does the FWHM rely only on the images, and not on variables and
contrasts?
 
Thank you very much!
Pedro Rosa.
 
On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote:
 
 Thanks, Doug!
 Should I run the mri_preproc and and smooth the output using
 mri_surf2surf with, let’s say, 10mm, and than run the LME normally in
 MatLab?
 Would this be problematic with a different smoothing procedure in
 mri_glmfit?
 How will mri_glmfit deal with the longitudinal design? Does this
 matter, or the FWHM would only be estimated on a average image of all
 time-points for all subjects?
 Regards,
 Pedro Rosa.
  
 On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote:
  
   
  I 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

On 04/15/2014 10:34 PM, Pedro Rosa wrote:
 Hi, Doug.
 Thanks a lot!
 The command would look like this: mri_glmfit-sim --glmdir 
 lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs 
 --overwrite --cache 1.3 abs
 It takes only a few seconds to run.
The command is fine, but remove --sim mc-z 1 2 teste. This tells it 
to do the simulation, which you don't need to do. It is overridden by 
the --cache flag. If they had occurred in the other order, you would be 
waiting days for the simulation to run.
 I have a few questions about how to run it:
 1) How the single entry for each subject look like in the FSGD file?
I'm not sure what you mean. Have you looked at the examples on the wiki?

 2) How to define the voxel/vertex-wise used to define clusters (after 
 —sim, -log10( p)), and the voxel-wise threshold for the —cache option?
 What is the difference between them?
They are the same
doug

 Thanks again,
 Pedro Rosa.

 On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote:


 On 04/14/2014 10:35 AM, Pedro Rosa wrote:
 Dear Doug and Jorge,
 I tried what you suggested and I think it work, although I have some
 concerns.
 I am working with a longitudinal study with two time-points for all
 subjects, three categorical variables (group, substance abuse /
 dependence and gender) and three continuous variables (interval
 between scans, age and medication intake).
 I generated a contrast with intercept + 7 betas for the LME, ran it
 without any problem and saved the sig.mgh using
 fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’).
 For the mri_glmfit I entered the same output from mri_surf2surf I used
 for the LME (smoothed at 10mm), but I did not know how exactly to
 enter the categorical and continuous variables, or which contrast to 
 use.
 I would do it as a paired-test (see the wiki). You may have to re-run
 mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this
 as the input to mri_glmfit. Set up the FSGD with the categorical and
 continuous variables (note that the FSGD file will have only a single
 entry per subject). Create your contrasts and run mri_glmfit. Overwrite
 the sig.mgh with the one from LME. Then run mri_glmfit-sim with the
 --cache option (not permutation)

 I don't know what your contrast of interest is, so I can't help you
 there. In the end, it does not matter because you are overwriting the
 sig map anyway. You just need a contrast as a place holder.

 doug

 The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch

 I just tested creating a matrix with 24 columns
 (Nclasses*(Nvariables+1) as suggested for DODS).
 Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir
 Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished
 apparently without errors.
 I attached the logs for both mri_glmfit and mri_glmfit-sim.

 That said, I have the following questions:

 1) What does the FWHM procedure does?
 2) How should I decide which contrast to test if the mri_glmfit does
 not consider the longitudinal design?
 3) Will the mri_glmfit-sim consider only the FMHM output from
 mri_glmfit and sig.mgh from the LME, or also other outputs from the
 mri_glmfit?
 4) Does the FWHM rely only on the images, and not on variables and
 contrasts?

 Thank you very much!
 Pedro Rosa.

 On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote:

 Thanks, Doug!
 Should I run the mri_preproc and and smooth the output using
 mri_surf2surf with, let’s say, 10mm, and than run the LME normally in
 MatLab?
 Would this be problematic with a different smoothing procedure in
 mri_glmfit?
 How will mri_glmfit deal with the longitudinal design? Does this
 matter, or the FWHM would only be estimated on a average image of all
 time-points for all subjects?
 Regards,
 Pedro Rosa.

 On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote:


 I think I would just run mri_glmfit on your data to get the proper
 directly structure and estimate of FWHM, then copy the sig file from
 the mixed fx analysis into the glmfit folder for one of the
 contrasts. Then run mri_glmfit-sim.

 doug


 On 3/29/14 10:29 AM, Pedro Rosa wrote:
 Dear Doug and Jorge,
 Thank you very much for your help.
 I found another message in the list
 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
  

 in which you suggested a way of using MC in mri_glmfit-sim by
 creating “fake files”, which would not be read by the script. In
 this case, only the simulation would be run, and not the full
 statistics. The command would be something like this:
 - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste
 --sim-sign abs
 I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as
 suggested by the older post. This would be fine, I believe, if only
 sig.mgh is read by the script.
 However, I get this message after running the command:

 [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa%
 mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste
 --sim-sign abs

 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Pedro Rosa]

Hi, Doug.  
Thanks a lot!
The command would look like this: mri_glmfit-sim --glmdir 
lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs --overwrite 
--cache 1.3 abs
It takes only a few seconds to run.
I have a few questions about how to run it:
1) How the single entry for each subject look like in the FSGD file?

2) How to define the voxel/vertex-wise used to define clusters (after —sim, 
-log10( p)), and the voxel-wise threshold for the —cache option?
What is the difference between them?

Thanks again,
Pedro Rosa.


On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote:

  
 On 04/14/2014 10:35 AM, Pedro Rosa wrote:
  Dear Doug and Jorge,
  I tried what you suggested and I think it work, although I have some  
  concerns.
  I am working with a longitudinal study with two time-points for all  
  subjects, three categorical variables (group, substance abuse /  
  dependence and gender) and three continuous variables (interval  
  between scans, age and medication intake).
  I generated a contrast with intercept + 7 betas for the LME, ran it  
  without any problem and saved the sig.mgh using  
  fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’).
  For the mri_glmfit I entered the same output from mri_surf2surf I used  
  for the LME (smoothed at 10mm), but I did not know how exactly to  
  enter the categorical and continuous variables, or which contrast to use.
   
  
 I would do it as a paired-test (see the wiki). You may have to re-run  
 mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this  
 as the input to mri_glmfit. Set up the FSGD with the categorical and  
 continuous variables (note that the FSGD file will have only a single  
 entry per subject). Create your contrasts and run mri_glmfit. Overwrite  
 the sig.mgh with the one from LME. Then run mri_glmfit-sim with the  
 --cache option (not permutation)
  
 I don't know what your contrast of interest is, so I can't help you  
 there. In the end, it does not matter because you are overwriting the  
 sig map anyway. You just need a contrast as a place holder.
  
 doug
  
  The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch
   
  I just tested creating a matrix with 24 columns  
  (Nclasses*(Nvariables+1) as suggested for DODS).
  Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir  
  Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished  
  apparently without errors.
  I attached the logs for both mri_glmfit and mri_glmfit-sim.
   
  That said, I have the following questions:
   
  1) What does the FWHM procedure does?
  2) How should I decide which contrast to test if the mri_glmfit does  
  not consider the longitudinal design?
  3) Will the mri_glmfit-sim consider only the FMHM output from  
  mri_glmfit and sig.mgh from the LME, or also other outputs from the  
  mri_glmfit?
  4) Does the FWHM rely only on the images, and not on variables and  
  contrasts?
   
  Thank you very much!
  Pedro Rosa.
   
  On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote:
   
   Thanks, Doug!
   Should I run the mri_preproc and and smooth the output using  
   mri_surf2surf with, let’s say, 10mm, and than run the LME normally in  
   MatLab?
   Would this be problematic with a different smoothing procedure in  
   mri_glmfit?
   How will mri_glmfit deal with the longitudinal design? Does this  
   matter, or the FWHM would only be estimated on a average image of all  
   time-points for all subjects?
   Regards,
   Pedro Rosa.

   On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote:

 
I think I would just run mri_glmfit on your data to get the proper  
directly structure and estimate of FWHM, then copy the sig file from  
the mixed fx analysis into the glmfit folder for one of the  
contrasts. Then run mri_glmfit-sim.
 
doug
 
 
On 3/29/14 10:29 AM, Pedro Rosa wrote:
 Dear Doug and Jorge,
 Thank you very much for your help.
 I found another message in the list  
 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
   
 in which you suggested a way of using MC in mri_glmfit-sim by  
 creating “fake files”, which would not be read by the script. In  
 this case, only the simulation would be run, and not the full  
 statistics. The command would be something like this:
 - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste  
 --sim-sign abs
 I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as  
 suggested by the older post. This would be fine, I believe, if only  
 sig.mgh is read by the script.
 However, I get this message after running the command:
  
 [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa%  
 mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste  
 --sim-sign abs
  
 if: Expression Syntax.
  
  
 Is it possible to do what I am trying to do? Does the residual  

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Pedro Rosa]

Dear Doug and Jorge,
I tried what you suggested and I think it work, although I have some concerns.I am working with a longitudinal study with two time-points for all subjects, three categorical variables (group, substance abuse / dependence and gender) and three continuous variables (interval between scans, age and medication intake).I generated a contrast with intercept + 7 betas for the LME, ran it without any problem and saved the sig.mgh using fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’).For the mri_glmfit I entered the same output from mri_surf2surf I used for the LME (smoothed at 10mm), but I did not know how exactly to enter the categorical and continuous variables, or which contrast to use.The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 schI just tested creating a matrix with 24 columns (Nclasses*(Nvariables+1) as suggested for DODS).Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished apparentlywithout errors.I attached the logs for both mri_glmfit and mri_glmfit-sim.That said, I have the following questions:1) What does the FWHM procedure does?2) How should I decide which contrast to test if the mri_glmfit does not consider the longitudinal design?3) Will the mri_glmfit-sim consider only the FMHM output from mri_glmfit and sig.mgh from the LME, or also other outputs from the mri_glmfit?4) Does the FWHM rely only on the images, and not on variables and contrasts?Thank you very much!Pedro Rosa.
 
On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote:



Thanks, Doug!
Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab?Would this be problematic with a different smoothing procedure in mri_glmfit?How will mri_glmfit deal with the longitudinal design? Does this matter, or the FWHM would only be estimated on a average image of all time-points for all subjects?Regards,Pedro Rosa.
  
On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote:






I think I would just run mri_glmfit on your data to get the proper
directly structure and estimate of FWHM, then copy the sig file from
the mixed fx analysis into the glmfit folder for one of the
contrasts. Then run mri_glmfit-sim.

doug


On 3/29/14 10:29 AM, Pedro Rosa wrote:

   Dear Doug and Jorge,
  Thank you very much for your help.
  I found another message in the list
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
in which you suggested a way of using MC in mri_glmfit-sim by
creating “fake files”, which would not be read by the script. In
this case, only the simulation would be run, and not the full
statistics. The command would be something like this:
  - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2
teste --sim-sign abs
  I created a “fake”mri_glmfit.log, fwhm.dat and mask.mgh
files as suggested by the older post. This would be fine, I
believe, if only sig.mgh is read by the script.
  However, I get this message after running the command:
  
[server:Long-T0-T2-Posproc/Vertex/Sch]
  pedrogomesrosa% mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim
  mc-full 5 2 teste --sim-sign abs
if:
  _expression_ Syntax.


Is it possible to do what I am trying to
  do? Does the residual errors at each location included in the
  sig.mgh, and, if necessary, how to compute it into image FWHM?
Regards,
  
  
Pedro Rosa.


  
  On Friday, March 28, 2014 at 2:38 PM,
Douglas N Greve wrote:

  

  Jorge, do you output the FWHM?
  doug
  
  
  On 03/27/2014 03:14 PM, jorge luis wrote:

  Hi Pedro
  
  
  Sorry, right now the only multiple comparisons
corrections implemented 
  in lme are the original Benjamini and Hochberg
(1995) FDR procedure 
  (lme_mass_FDR) and a more recent and powerful
two-stage FDR procedure 
  (lme_mass_FDR2):
  
  
  Benjamini, Y., Krieger, A.M., Yekutieli, D.
(2006). Adaptive linear 
  step-up procedures that control the false
discovery rate. Biometrika, 
  93, 491-507.
  
  
  In my 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

On 04/14/2014 10:35 AM, Pedro Rosa wrote:
 Dear Doug and Jorge,
 I tried what you suggested and I think it work, although I have some 
 concerns.
 I am working with a longitudinal study with two time-points for all 
 subjects, three categorical variables (group, substance abuse / 
 dependence and gender) and three continuous variables (interval 
 between scans, age and medication intake).
 I generated a contrast with intercept + 7 betas for the LME, ran it 
 without any problem and saved the sig.mgh using 
 fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’).
 For the mri_glmfit I entered the same output from mri_surf2surf I used 
 for the LME (smoothed at 10mm), but I did not know how exactly to 
 enter the categorical and continuous variables, or which contrast to use.
I would do it as a paired-test (see the wiki). You may have to re-run 
mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this 
as the input to mri_glmfit. Set up the FSGD with the categorical and 
continuous variables (note that the FSGD file will have only a single 
entry per subject). Create your contrasts and run mri_glmfit. Overwrite 
the sig.mgh with the one from LME. Then run mri_glmfit-sim with the 
--cache option (not permutation)

I don't know what your contrast of interest is, so I can't help you 
there. In the end, it does not matter because you are overwriting the 
sig map anyway. You just need a contrast as a place holder.

doug

 The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch

 I just tested creating a matrix with 24 columns 
 (Nclasses*(Nvariables+1) as suggested for DODS).
 Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir 
 Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished 
 apparently without errors.
 I attached the logs for both mri_glmfit and mri_glmfit-sim.

 That said, I have the following questions:

 1) What does the FWHM procedure does?
 2) How should I decide which contrast to test if the mri_glmfit does 
 not consider the longitudinal design?
 3) Will the mri_glmfit-sim consider only the FMHM output from 
 mri_glmfit and sig.mgh from the LME, or also other outputs from the 
 mri_glmfit?
 4) Does the FWHM rely only on the images, and not on variables and 
 contrasts?

 Thank you very much!
 Pedro Rosa.

 On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote:

 Thanks, Doug!
 Should I run the mri_preproc and and smooth the output using 
 mri_surf2surf with, let’s say, 10mm, and than run the LME normally in 
 MatLab?
 Would this be problematic with a different smoothing procedure in 
 mri_glmfit?
 How will mri_glmfit deal with the longitudinal design? Does this 
 matter, or the FWHM would only be estimated on a average image of all 
 time-points for all subjects?
 Regards,
 Pedro Rosa.

 On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote:


 I think I would just run mri_glmfit on your data to get the proper 
 directly structure and estimate of FWHM, then copy the sig file from 
 the mixed fx analysis into the glmfit folder for one of the 
 contrasts. Then run mri_glmfit-sim.

 doug


 On 3/29/14 10:29 AM, Pedro Rosa wrote:
 Dear Doug and Jorge,
 Thank you very much for your help.
 I found another message in the list 
 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
  
 in which you suggested a way of using MC in mri_glmfit-sim by 
 creating “fake files”, which would not be read by the script. In 
 this case, only the simulation would be run, and not the full 
 statistics. The command would be something like this:
 - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste 
 --sim-sign abs
 I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as 
 suggested by the older post. This would be fine, I believe, if only 
 sig.mgh is read by the script.
 However, I get this message after running the command:

 [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% 
 mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste 
 --sim-sign abs

 if: Expression Syntax.


 Is it possible to do what I am trying to do? Does the residual 
 errors at each location included in the sig.mgh, and, if necessary, 
 how to compute it into image FWHM?

 Regards,

 Pedro Rosa.

 On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote:

 Jorge, do you output the FWHM?
 doug

 On 03/27/2014 03:14 PM, jorge luis wrote:
 Hi Pedro

 Sorry, right now the only multiple comparisons corrections 
 implemented
 in lme are the original Benjamini and Hochberg (1995) FDR procedure
 (lme_mass_FDR) and a more recent and powerful two-stage FDR 
 procedure
 (lme_mass_FDR2):

 Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear
 step-up procedures that control the false discovery rate. 
 Biometrika,
 93, 491-507.

 In my experience, this procedure is as powerful to detect effects in
 neuroimage data as alternative corrections with strong control of 
 the
 family-wise error rate (FWE). However it would be great if we 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Pedro Rosa]

Thanks, Doug!  
Should I run the mri_preproc and and smooth the output using mri_surf2surf 
with, let’s say, 10mm, and than run the LME normally in MatLab?
Would this be problematic with a different smoothing procedure in mri_glmfit?
How will mri_glmfit deal with the longitudinal design? Does this matter, or the 
FWHM would only be estimated on a average image of all time-points for all 
subjects?
Regards,
Pedro Rosa.


On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote:

  
 I think I would just run mri_glmfit on your data to get the proper directly 
 structure and estimate of FWHM, then copy the sig file from the mixed fx 
 analysis into the glmfit folder for one of the contrasts. Then run 
 mri_glmfit-sim.
  
 doug
  
  
 On 3/29/14 10:29 AM, Pedro Rosa wrote:
  Dear Doug and Jorge,  
  Thank you very much for your help.
  I found another message in the list 
  (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
   in which you suggested a way of using MC in mri_glmfit-sim by creating 
  “fake files”, which would not be read by the script. In this case, only the 
  simulation would be run, and not the full statistics. The command would be 
  something like this:
  - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign 
  abs
  I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested 
  by the older post. This would be fine, I believe, if only sig.mgh is read 
  by the script.
  However, I get this message after running the command:
  [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim 
  --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs
  if: Expression Syntax.
   
  Is it possible to do what I am trying to do? Does the residual errors at 
  each location included in the sig.mgh, and, if necessary, how to compute it 
  into image FWHM?  
  Regards,
   
  Pedro Rosa.
   
   
  On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote:
   
   Jorge, do you output the FWHM?
   doug

   On 03/27/2014 03:14 PM, jorge luis wrote:
Hi Pedro
 
Sorry, right now the only multiple comparisons corrections implemented  
in lme are the original Benjamini and Hochberg (1995) FDR procedure  
(lme_mass_FDR) and a more recent and powerful two-stage FDR procedure  
(lme_mass_FDR2):
 
Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear  
step-up procedures that control the false discovery rate. Biometrika,  
93, 491-507.
 
In my experience, this procedure is as powerful to detect effects in  
neuroimage data as alternative corrections with strong control of the  
family-wise error rate (FWE). However it would be great if we could  
use an implementation of any multiple comparisons correction with  
strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures  
only provide weak control). The residual errors at each location  
required to compute an estimate of the image FWHM can be obtained from  
the lme output. But an actual FWHM estimate is not currently saved.
 
Best  
-Jorge
 
 
El Martes 25 de marzo de 2014 8:15, Pedro Rosa  
pedrogomesr...@gmail.com (mailto:pedrogomesr...@gmail.com) escribió:
 
Dear Doug,  
Thank you very much!
I will try what you suggested, although I am not sure if Jorge's
stream outputs the FMHM, or if I would need to run the statistics
from the beggining using in the terminal, and not in MatLab.
Do you think Jorge could comment on this issue?
Regards,
Pedro Rosa.
 
On Mar 24, 2014, at 12:44 PM, Douglas Greve  
gr...@nmr.mgh.harvard.edu (mailto:gr...@nmr.mgh.harvard.edu) 
mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
In theory, it should be possible. I have not used Jorge's stream,  
so I
don't know that much about it. Does it save an estimate of the
FWHM? If
so, then you can run mri_surfcluster passing it the p-value (ie,
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold.
This is
what mri_glmfit-sim does, so you might check that script for
mri_surfcluster command line options
 
doug  
 
 
 On 3/22/14 11:03 PM, Pedro Rosa wrote:  
 Dear list,
 I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline
in a structural MRI dataset and I would like to use Monte Carlo as
the method for correction for multiple comparisons. However, the
longitudinal LME tutorial includes only FDR correction
(lme_mass_FDR2).
 Is it possible to use Monte Carlo correction for longitudinal
data? Can I input the outputs from MatLab (fstats =
lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and
then run Monte Carlo?
 If not, do you have any other suggestions of how I use Monte
Carlo in longitudinal analyses?
 Thanks in advance,
 
___  

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas Greve]

I think I would just run mri_glmfit on your data to get the proper 
directly structure and estimate of FWHM, then copy the sig file from the 
mixed fx analysis into the glmfit folder for one of the contrasts. Then 
run mri_glmfit-sim.


doug


On 3/29/14 10:29 AM, Pedro Rosa wrote:

Dear Doug and Jorge,
Thank you very much for your help.
I found another message in the list 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) 
in which you suggested a way of using MC in mri_glmfit-sim by creating 
fake files, which would not be read by the script. In this case, 
only the simulation would be run, and not the full statistics. The 
command would be something like this:
- mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste 
--sim-sign abs
I created a fake mri_glmfit.log, fwhm.dat and mask.mgh files as 
suggested by the older post. This would be fine, I believe, if only 
sig.mgh is read by the script.

However, I get this message after running the command:

[server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim 
--glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs


if: Expression Syntax.


Is it possible to do what I am trying to do? Does the residual errors 
at each location included in the sig.mgh, and, if necessary, how to 
compute it into image FWHM?


Regards,

Pedro Rosa.

On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote:


Jorge, do you output the FWHM?
doug

On 03/27/2014 03:14 PM, jorge luis wrote:

Hi Pedro

Sorry, right now the only multiple comparisons corrections implemented
in lme are the original Benjamini and Hochberg (1995) FDR procedure
(lme_mass_FDR) and a more recent and powerful two-stage FDR procedure
(lme_mass_FDR2):

Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear
step-up procedures that control the false discovery rate. Biometrika,
93, 491-507.

In my experience, this procedure is as powerful to detect effects in
neuroimage data as alternative corrections with strong control of the
family-wise error rate (FWE). However it would be great if we could
use an implementation of any multiple comparisons correction with
strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures
only provide weak control). The residual errors at each location
required to compute an estimate of the image FWHM can be obtained from
the lme output. But an actual FWHM estimate is not currently saved.

Best
-Jorge


El Martes 25 de marzo de 2014 8:15, Pedro Rosa
pedrogomesr...@gmail.com mailto:pedrogomesr...@gmail.com escribió:

Dear Doug,
Thank you very much!
I will try what you suggested, although I am not sure if Jorge's
stream outputs the FMHM, or if I would need to run the statistics
from the beggining using in the terminal, and not in MatLab.
Do you think Jorge could comment on this issue?
Regards,
Pedro Rosa.

On Mar 24, 2014, at 12:44 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


In theory, it should be possible. I have not used Jorge's stream,
so I
don't know that much about it. Does it save an estimate of the
FWHM? If
so, then you can run mri_surfcluster passing it the p-value (ie,
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold.
This is
what mri_glmfit-sim does, so you might check that script for
mri_surfcluster command line options

doug


 On 3/22/14 11:03 PM, Pedro Rosa wrote:
 Dear list,
 I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline
in a structural MRI dataset and I would like to use Monte Carlo as
the method for correction for multiple comparisons. However, the
longitudinal LME tutorial includes only FDR correction
(lme_mass_FDR2).
 Is it possible to use Monte Carlo correction for longitudinal
data? Can I input the outputs from MatLab (fstats =
lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and
then run Monte Carlo?
 If not, do you have any other suggestions of how I use Monte
Carlo in longitudinal analyses?
 Thanks in advance,

___
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Pedro Rosa]

Dear Doug and Jorge,
Thank you very much for your help.
I found another message in the list 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
 in which you suggested a way of using MC in mri_glmfit-sim by creating “fake 
files”, which would not be read by the script. In this case, only the 
simulation would be run, and not the full statistics. The command would be 
something like this:
- mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs
I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested by 
the older post. This would be fine, I believe, if only sig.mgh is read by the 
script.
However, I get this message after running the command:
[server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim --glmdir 
$SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs
if: Expression Syntax.

Is it possible to do what I am trying to do? Does the residual errors at each 
location included in the sig.mgh, and, if necessary, how to compute it into 
image FWHM?
Regards,

Pedro Rosa.


On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote:

 Jorge, do you output the FWHM?
 doug
  
 On 03/27/2014 03:14 PM, jorge luis wrote:
  Hi Pedro
   
  Sorry, right now the only multiple comparisons corrections implemented  
  in lme are the original Benjamini and Hochberg (1995) FDR procedure  
  (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure  
  (lme_mass_FDR2):
   
  Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear  
  step-up procedures that control the false discovery rate. Biometrika,  
  93, 491-507.
   
  In my experience, this procedure is as powerful to detect effects in  
  neuroimage data as alternative corrections with strong control of the  
  family-wise error rate (FWE). However it would be great if we could  
  use an implementation of any multiple comparisons correction with  
  strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures  
  only provide weak control). The residual errors at each location  
  required to compute an estimate of the image FWHM can be obtained from  
  the lme output. But an actual FWHM estimate is not currently saved.
   
  Best
  -Jorge
   
   
  El Martes 25 de marzo de 2014 8:15, Pedro Rosa  
  pedrogomesr...@gmail.com (mailto:pedrogomesr...@gmail.com) escribió:
   
  Dear Doug,
  Thank you very much!
  I will try what you suggested, although I am not sure if Jorge's
  stream outputs the FMHM, or if I would need to run the statistics
  from the beggining using in the terminal, and not in MatLab.
  Do you think Jorge could comment on this issue?
  Regards,
  Pedro Rosa.
   
  On Mar 24, 2014, at 12:44 PM, Douglas Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
   
   
  In theory, it should be possible. I have not used Jorge's stream,
  so I
  don't know that much about it. Does it save an estimate of the
  FWHM? If
  so, then you can run mri_surfcluster passing it the p-value (ie,
  -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold.
  This is
  what mri_glmfit-sim does, so you might check that script for
  mri_surfcluster command line options
   
  doug
   
   
   On 3/22/14 11:03 PM, Pedro Rosa wrote:
   Dear list,
   I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline
  in a structural MRI dataset and I would like to use Monte Carlo as
  the method for correction for multiple comparisons. However, the
  longitudinal LME tutorial includes only FDR correction
  (lme_mass_FDR2).
   Is it possible to use Monte Carlo correction for longitudinal
  data? Can I input the outputs from MatLab (fstats =
  lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and
  then run Monte Carlo?
   If not, do you have any other suggestions of how I use Monte
  Carlo in longitudinal analyses?
   Thanks in advance,
   
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  The information in this e-mail is intended only for the person to
  whom it is
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  the e-mail
  contains patient information, please contact the Partners
  Compliance HelpLine at
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

Jorge, do you output the FWHM?
doug

On 03/27/2014 03:14 PM, jorge luis wrote:
 Hi Pedro

 Sorry, right now the only multiple comparisons corrections implemented 
 in lme are the original Benjamini and Hochberg (1995) FDR procedure 
 (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure 
 (lme_mass_FDR2):

 Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear 
 step-up procedures that control the false discovery rate. Biometrika, 
 93, 491-507.

 In my experience, this procedure is as powerful to detect effects in 
 neuroimage data as alternative corrections with strong control of the 
 family-wise error rate (FWE).  However it would be great if we could 
 use an implementation of any multiple comparisons correction with 
 strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures 
 only provide weak control). The residual errors at each location 
 required to compute an estimate of the image FWHM can be obtained from 
 the lme output. But an actual FWHM estimate is not currently saved.

 Best
 -Jorge


 El Martes 25 de marzo de 2014 8:15, Pedro Rosa 
 pedrogomesr...@gmail.com escribió:

 Dear Doug,
 Thank you very much!
 I will try what you suggested,  although I am not sure if Jorge's
 stream outputs the FMHM, or if I would need to run the statistics
 from the beggining using in the terminal, and not in MatLab.
 Do you think Jorge could comment on this issue?
 Regards,
 Pedro Rosa.

 On Mar 24, 2014, at 12:44 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 In theory, it should be possible. I have not used Jorge's stream,
 so I
 don't know that much about it. Does it save an estimate of the
 FWHM? If
 so, then you can run mri_surfcluster passing it the p-value (ie,
 -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold.
 This is
 what mri_glmfit-sim does, so you might check that script for
 mri_surfcluster command line options

 doug


  On 3/22/14 11:03 PM, Pedro Rosa wrote:
  Dear list,
  I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline
 in a structural MRI dataset and I would like to use Monte Carlo as
 the method for correction for multiple comparisons. However, the
 longitudinal LME tutorial includes only FDR correction
 (lme_mass_FDR2).
  Is it possible to use Monte Carlo correction for longitudinal
 data? Can I input the outputs from MatLab (fstats =
 lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and
 then run Monte Carlo?
  If not, do you have any other suggestions of how I use Monte
 Carlo in longitudinal analyses?
  Thanks in advance,

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 The information in this e-mail is intended only for the person to
 whom it is
 addressed. If you believe this e-mail was sent to you in error and
 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to
 you in error
 but does not contain patient information, please contact the
 sender and properly
 dispose of the e-mail.



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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[jorge luis]

Hi Pedro

Sorry, right now the only multiple comparisons corrections implemented in lme 
are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and 
a more recent and powerful two-stage FDR procedure (lme_mass_FDR2):

Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear step-up 
procedures that control the false discovery rate. Biometrika, 93, 491-507.

In my experience, this procedure is as powerful to detect effects in neuroimage 
data as alternative corrections with strong control of the family-wise error 
rate (FWE).  However it would be great if we could use an implementation of any 
multiple comparisons correction with strong control of the FWE (MC, RFT, 
ect...) for lme (FDR procedures only provide weak control). The residual errors 
at each location required to compute an estimate of the image FWHM can be 
obtained from the lme output. But an actual FWHM estimate is not currently 
saved.


Best
-Jorge




El Martes 25 de marzo de 2014 8:15, Pedro Rosa pedrogomesr...@gmail.com 
escribió:
 
Dear Doug,
Thank you very much!
I will try what you suggested,  although I am not sure if Jorge's stream 
outputs the FMHM, or if I would need to run the statistics from the beggining 
using in the terminal, and not in MatLab.
Do you think Jorge could comment on this issue?
Regards,
Pedro Rosa.

On Mar 24, 2014, at 12:44 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:


In theory, it should be possible. I have not used Jorge's stream, so I 
don't know that much about it. Does it save an estimate of the FWHM? If 
so, then you can run mri_surfcluster passing it the p-value (ie, 
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is 
what mri_glmfit-sim does, so you might check that script for 
mri_surfcluster command line options

doug


 On 3/22/14 11:03 PM, Pedro Rosa wrote:
 Dear list,
 I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a 
 structural MRI dataset and I would like to use Monte Carlo as the method for 
 correction for multiple comparisons. However, the longitudinal LME tutorial 
 includes only FDR correction (lme_mass_FDR2).
 Is it possible to use Monte Carlo correction for longitudinal data? Can I 
 input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / 
 sgn / df) into mri_glmfit and then run Monte Carlo?
 If not, do you have any other suggestions of how I use Monte Carlo in 
 longitudinal analyses?
 Thanks in advance,

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine 
at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and 
properly
dispose of the e-mail.



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Pedro Rosa]

Dear Doug,
Thank you very much!
I will try what you suggested,  although I am not sure if Jorge's stream 
outputs the FMHM, or if I would need to run the statistics from the beggining 
using in the terminal, and not in MatLab.
Do you think Jorge could comment on this issue?
Regards,
Pedro Rosa.

On Mar 24, 2014, at 12:44 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:


In theory, it should be possible. I have not used Jorge's stream, so I 
don't know that much about it. Does it save an estimate of the FWHM? If 
so, then you can run mri_surfcluster passing it the p-value (ie, 
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is 
what mri_glmfit-sim does, so you might check that script for 
mri_surfcluster command line options

doug


 On 3/22/14 11:03 PM, Pedro Rosa wrote:
 Dear list,
 I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a 
 structural MRI dataset and I would like to use Monte Carlo as the method for 
 correction for multiple comparisons. However, the longitudinal LME tutorial 
 includes only FDR correction (lme_mass_FDR2).
 Is it possible to use Monte Carlo correction for longitudinal data? Can I 
 input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / 
 sgn / df) into mri_glmfit and then run Monte Carlo?
 If not, do you have any other suggestions of how I use Monte Carlo in 
 longitudinal analyses?
 Thanks in advance,

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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