Re: [Freesurfer] Hippocampal subfield segmentation with T1 and T2

[Iglesias Gonzalez, Eugenio]

Hi Cassie,
It seems to be a problem with mri_robust_register, when trying to allíen the t1 
and t2 scans.
Martin, any ideas?

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Cassandra Wannan 

Sent: Thursday, January 18, 2018 10:59:45 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfield segmentation with T1 and T2

Hi all,

I've been trying to run the hippocampal subfield segmentation with T1 and T2 
images, and haven't had much luck. I had previously run recon-all on all my 
scans in v5.3, but testing on one subject I re-ran recon-all with the 
additional T2 scan, and that seems to have run fine. However, when I try to run 
the subfield segmentation, I am getting errors. My command line is:

recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz CRC040T1T2 
-no-isrunning

but I have also tried:

recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz 
CRC040T1T2 -no-isrunning

and:

recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2 
-no-isrunning

The error I am getting is:

/Applications/freesurfer_v6/bin//mri_robust_register --mov 
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz --maskmov 
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz
 --dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz --lta 
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta
 --noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file 
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta
gunzip: can't stat: 
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz
 
(/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz):
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192)

MATLAB:badSwitchExpression



Any idea what could be causing the issue? The hippocampal pipeline runs fine 
without the T2 scan, however I am planning to use the subfield segmentation as 
a mask for some white matter tractography analysis in FSL, and the dimensions 
of the output are not close to my nifti files. I was hoping that using the T2 
registration would help with this, but can't get it to work! Any help would be 
greatly appreciated.

Kind regards,

Cassie

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Re: [Freesurfer] Using subject specific template, atlas, & TPM

[Ramesh Babu]

Dear Bruce and Douglas,

Thank you for your suggestions. I am trying it and will need your
suggestions on result.

Thank you
Ramesh

On Fri, Jan 19, 2018 at 2:08 AM, Douglas Greve 
wrote:

> you can use gcatrain (and jkgcatrain for testing) if you are using v6
>
> On 1/12/18 3:27 PM, Bruce Fischl wrote:
>
> Hi Ramesh
>
> if you have segmentations in our aseg format (or edited asegs for that
> matter if you find them not accurate enough), you should be able to use
> mri_ca_train to genenerate a new .gca file and apply it to your subjects.
> Read the help and wiki and see if you can make it work, and let us knof i
> you have any issues. There are also surface-based atlases, but I suspect
> thos are a lot less likely to be biased by brain shape (since we map to a
> sphere anyway)
>
> cheers
> Bruce
> On Fri, 12 Jan 2018, Ramesh Babu wrote:
>
> Dear Bruce,
> Thank you for your prompt response. I have 2 groups & 40 subjects in each
> groups in my study. I am
> using freesurfer and various other software for analysis. I found that the
> template available for
> registration either western or Chinese. There is no template available for
> Indian brain population.
> Therefore we want to develop a template specific to our population. And we
> have created templates
> using different software and want to compare the result with default
> template (western brain
> template) and our template. I need your help how to use this template in
> freesurfer. As you
> mentioned in the previous mail I will try with training utility
> (mri_ca_train). Can I get any user
> guide to know details about it?
>
> Thank you
> Ramesh
>
> On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl
>   wrote:
>   Hi Ramesh
>
>   what are you trying to achieve? Our segmentation tools use their own
> format as they need
>   information not contained in most standard images, so it won't be
> easy to get it into
>   that format unless you use our training utility (mri_ca_train)
>
>   cheers
>   Bruce
>   On Thu, 11 Jan 2018, Ramesh Babu wrote:
>
> Dear experts,
> I have analysed T1 data using Freesurfer. Now we have created
> atlas,
> template & tissue probability
> map using different methods and softwares. I need your help to
> use template
> in freesufer, so that we
> can compare with default template and our template. Please
> help me to put
> these images in
> appropriate folders in Freesurfer.
>
>
> Thank you
> RB
>
>
>
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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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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[Freesurfer] Hippocampal subfield segmentation with T1 and T2

[Cassandra Wannan]

Hi all,

I've been trying to run the hippocampal subfield segmentation with T1 and
T2 images, and haven't had much luck. I had previously run recon-all on all
my scans in v5.3, but testing on one subject I re-ran recon-all with the
additional T2 scan, and that seems to have run fine. However, when I try to
run the subfield segmentation, I am getting errors. My command line is:

recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz
CRC040T1T2 -no-isrunning

but I have also tried:

recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz
CRC040T1T2 -no-isrunning

and:

recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2
-no-isrunning

The error I am getting is:

/Applications/freesurfer_v6/bin//mri_robust_register --mov
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz
--maskmov
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz
--dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz
--lta
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta
--noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta
gunzip: can't stat:
/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz
(/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz):
No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192)

MATLAB:badSwitchExpression



Any idea what could be causing the issue? The hippocampal pipeline runs
fine without the T2 scan, however I am planning to use the subfield
segmentation as a mask for some white matter tractography analysis in FSL,
and the dimensions of the output are not close to my nifti files. I was
hoping that using the T2 registration would help with this, but can't get
it to work! Any help would be greatly appreciated.

Kind regards,

Cassie
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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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Re: [Freesurfer] PET partial volume correction

[Douglas Greve]

It is a little tricky because you don't want to use different masks for 
different subjects. I recommend using CVS where I've created a 
subcoritcal mask in 2mm space (mri.2mm). So the idea would be that you 
map your subcortical MG map to CVS space, then smooth it (mri_fwhm) 
specifying the subcortical mask in 
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm. You can then 
concatenate the different subjects together to do your group analysis



On 1/18/18 5:14 PM, John Anderson wrote:

Dear Dr Greve,
Thank you so much for the quick response.

Just to confirm that I understood the procedure correctly. The 
analysis is volume based (i.e. voxel-wise) for the subcortical 
structures using mask created by freesurfer's "mri_binarize" for these 
regions.


Correct?

 Original Message 
On January 18, 2018 4:34 PM, John Anderson 
 wrote:

It is volume-based for subcortical


On 1/12/18 8:17 AM, John Anderson wrote:


Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume 
correction methods lead to different conclusions: An (18)F-FDG-PET 
study of aging" Thank you for publishing this data.


I understood from this paper that he recommended stream for PVC is to 
correct the PET images using Muller-Gartner method then feed the 
corrected maps into three group level analyses: surface based for 
left and right hemispheres then for subcortical regions..


My question is about the subcortical analysis: To describe this 
analysis, is it a volumetric analysis for subcortical gray matter, or 
surface based?


I am sorry if my questions is basics, I don't have good experience in 
freesurfer so I want to be sure that I am using the correct terms.


Thanks you for any advice!
John





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Re: [Freesurfer] PET partial volume correction

[John Anderson]

Dear Dr Greve,
Thank you so much for the quick response.

Just to confirm that I understood the procedure correctly. The analysis is 
volume based (i.e. voxel-wise) for the subcortical structures using mask 
created by freesurfer's "mri_binarize" for these regions.

Correct?

 Original Message 
On January 18, 2018 4:34 PM, John Anderson  wrote:
It is volume-based for subcortical

On 1/12/18 8:17 AM, John Anderson wrote:

> Dear Dr Greeve,
> I interestingly read the manuscript "Different partial volume correction 
> methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank 
> you for publishing this data.
>
> I understood from this paper that he recommended stream for PVC is to correct 
> the PET images using Muller-Gartner method then feed the corrected maps into 
> three group level analyses: surface based for left and right hemispheres then 
> for subcortical regions..
>
> My question is about the subcortical analysis: To describe this analysis, is 
> it a volumetric analysis for subcortical gray matter, or surface based?
>
> I am sorry if my questions is basics, I don't have good experience in 
> freesurfer so I want to be sure that I am using the correct terms.
>
> Thanks you for any advice!
> John___
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Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[Douglas Greve]

Is the problem that the surfreg command is failing or that you don't 
know how to apply LME?



On 1/17/18 9:55 AM, lanbo Wang wrote:

Hi Martin,

I didn't try to run recon-all, I try to run flipped.
The code I used is:
foreach subject (subj_27_2.long.s27_base)
foreach?   surfreg --s $subject --t fsaverage_sym --lh
foreach?   surfreg --s $subject --t fsaverage_sym --lh --xhemi
foreach? end


Thanks,
Lanbo

On Tue, Jan 16, 2018 at 4:46 AM, Martin Reuter 
> wrote:


Hi Lanbo,

what is the exact command you use for this? The problem is that
the script or your command does not pass the right flags to recon
all. Whenever recon-all is supposed to work on a longitudinal
directory it needs to know the base and the long so the recon all
command needs to show

-long subj_02_1 s02_base

as part of its arguments. So either adjust your command line, or
if the recon-all call is performed from within another script, we
need to change that script (add a -long flag so that the script
performs the correct recon-all call in those cases when working on
a longitudinal time point).

Once you have the left right difference (define on one of the
hemispheres), you can treat it similar as a thickness map and run
it through the Matlab LME code.
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels



Best, Martin


Am 27.12.2017 um 16:11 schrieb lanbo Wang:

Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it
showed error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to
/HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz...
Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

Secondly, how I can get the change rate after construct left
-right registration.

Thanks,
Lanbo

On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter
> wrote:

Hi Lanbo,

you could look at longitudinal changes of the left-right
difference in volume per ROI. Or do you mean on the cortical
thickness map (I have never done that, but probably works
similarly, construct left -right registration, compute
difference, then run the LME on that).

Best, Martin


Am 17.12.2017 um 17:54 schrieb lanbo Wang:

Hi, all experts.
I want to compare changes rate between left and right
hemisphere of longitudinal data, How should I do that, how
to combine xhemi with two stage or LME?

Best,
Lanbo


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Re: [Freesurfer] PET partial volume correction

[Douglas Greve]

It is volume-based for subcortical


On 1/12/18 8:17 AM, John Anderson wrote:

Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume 
correction methods lead to different conclusions: An (18)F-FDG-PET 
study of aging" Thank you for publishing this data.


I understood from this paper that he recommended stream for PVC is to 
correct the PET images using Muller-Gartner method then feed the 
corrected maps into three group level analyses: surface based for left 
and right hemispheres then for subcortical regions..


My question is about the subcortical analysis: To describe this 
analysis, is it a volumetric analysis for subcortical gray matter, or 
surface based?


I am sorry if my questions is basics, I don't have good experience in 
freesurfer so I want to be sure that I am using the correct terms.


Thanks you for any advice!
J


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Re: [Freesurfer] mri_coreg

[Douglas Greve]

No, sorry. You have to use mri_vol2vol. Should be pretty simple

On 1/18/18 4:34 PM, John Anderson wrote:

Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the 
registered images. I mean flag "--out or -o" similar to spmregister?


Thanks for any guidance
John


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[Freesurfer] mri_coreg

[John Anderson]

Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the registered 
images. I mean flag "--out or -o" similar to spmregister?

Thanks for any guidance
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[Freesurfer] PET partial volume correction

[John Anderson]

Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction 
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank 
you for publishing this data.

I understood from this paper that he recommended stream for PVC is to correct 
the PET images using Muller-Gartner method then feed the corrected maps into 
three group level analyses: surface based for left and right hemispheres then 
for subcortical regions..

My question is about the subcortical analysis: To describe this analysis, is it 
a volumetric analysis for subcortical gray matter, or surface based?

I am sorry if my questions is basics, I don't have good experience in 
freesurfer so I want to be sure that I am using the correct terms.

Thanks you for any advice!
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Re: [Freesurfer] motion parameter in preprocessing stream

[Douglas Greve]

I don't think so, sorry


On 1/18/18 8:58 AM, Carme Uribe Codesal wrote:

Dear all FreeSurfer users,

I was wondering if I can extract any parameter of movement from the 
recon-all processing using FreeSurfer 5.1.


Thanks in advance!

Kind regards,

Carme


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Re: [Freesurfer] aparcstats2table

[Douglas Greve]

Why don't you just create a fake directory structure. Should be pretty 
easy to script (if you know how to script:)



On 1/15/18 3:44 AM, Stephanos Leandrou wrote:


Dear Freesurfer Developers,

I want to use the asegstats2table and aparcstats2table for my 
research. First of all, my subjects (several hundreds) are not in the 
Freesurfer/Subjects directory and for each one I have run the 
recon-all command.


For the asegstats2table command we know that the subjects list can be 
specified in one of four ways:


 1. Specify each subject after -s
  * -s subject1 -s subject2 ..
 2. specify all subjects after --subjects.
  * --subjects does not have to be the last argument. Eg:
  o --subjects subject1 subject2 ...
 3. Specify each input file after -i
  * -i subject1/stats/aseg.stats -i subject2/stat/aseg.stats ..
 4. Specify all the input stat files after --inputs. --inputs does not
have
  * to be the last argument. Eg:
  o --inputs subject1/stats/aseg.stats
subject2/stats/aseg.stats ...

The first two methods assume the freesurfer directory structure. 
The last two are general and can be used with any file produced 
by mri_segstats regardless of whether it was created with recon-all or 
not…..


According to 3 and 4 by changing –subjects to –i I was able to run the 
asegstats2table command for my subjects that are not in the Freesurfer 
directory structure with success.


However, (and here comes my question) I cannot do the same for the 
aparcstats2table because there is no option (if I am not mistaken) to 
run the command for subjects outside the Freesurfer directory 
structure? In the aparcstats2table webpage mentions that the subjects 
list can be specified on either of two ways:


 1. Specify each subject after a -s flag
  * -s subject1 -s subject2 ... --hemi lh
 2. Specify all subjects after --subjects flag. --subjects does not have
  * to be the last argument. Eg:
  o --subject subject1 subject2 ... --hemi lh

However, when I run the command (in the path of my subjects directory 
where the stats folder is) it comes with an error which says that it 
cannot find the stats file in the Freesurfer/directory which is 
expected…as my subjects are not in that directory.


Thank you for your help !!

Stephanos



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Re: [Freesurfer] Using subject specific template, atlas, & TPM

[Douglas Greve]

you can use gcatrain (and jkgcatrain for testing) if you are using v6


On 1/12/18 3:27 PM, Bruce Fischl wrote:

Hi Ramesh

if you have segmentations in our aseg format (or edited asegs for that 
matter if you find them not accurate enough), you should be able to 
use mri_ca_train to genenerate a new .gca file and apply it to your 
subjects. Read the help and wiki and see if you can make it work, and 
let us knof i you have any issues. There are also surface-based 
atlases, but I suspect thos are a lot less likely to be biased by 
brain shape (since we map to a sphere anyway)


cheers
Bruce
On Fri, 12 Jan 2018, Ramesh Babu wrote:


Dear Bruce,
Thank you for your prompt response. I have 2 groups & 40 subjects in 
each groups in my study. I am
using freesurfer and various other software for analysis. I found 
that the template available for
registration either western or Chinese. There is no template 
available for Indian brain population.
Therefore we want to develop a template specific to our population. 
And we have created templates
using different software and want to compare the result with default 
template (western brain
template) and our template. I need your help how to use this template 
in freesurfer. As you
mentioned in the previous mail I will try with training utility 
(mri_ca_train). Can I get any user

guide to know details about it?

Thank you
Ramesh

On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl 
 wrote:

  Hi Ramesh

  what are you trying to achieve? Our segmentation tools use 
their own format as they need
  information not contained in most standard images, so it won't 
be easy to get it into

  that format unless you use our training utility (mri_ca_train)

  cheers
  Bruce
  On Thu, 11 Jan 2018, Ramesh Babu wrote:

    Dear experts,
    I have analysed T1 data using Freesurfer. Now we have 
created atlas,

    template & tissue probability
    map using different methods and softwares. I need your 
help to use template

    in freesufer, so that we
    can compare with default template and our template. 
Please help me to put

    these images in
    appropriate folders in Freesurfer.


    Thank you
    RB



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Re: [Freesurfer] Jittering Fixation Time

[Douglas Greve]

That is fine


On 1/12/18 2:26 PM, Ashley Cole wrote:

Dear FreeSurfer Experts,

I have a question about jittering the fixation point and how 
Freesurfer handles it.


Is it ok to have different rest times in the paradigm file for FS-FAST 
pipeline? In the paradigm file, I am giving it an actual onset time 
and for the length of the rest block I am giving it a length that has 
been jittered and sometimes this length is a multiple of the TR and 
sometimes is not.


Is this ok?


Thank you,

Ash


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Re: [Freesurfer] ROI statistics and median values

[Douglas Greve]

I don't think we have anything. You can do it in matlab, eg

aseg = MRIread('aseg.mgz');

vol = MRIread('vol.nii.gz');

ind = find(aseg.vol==17); % left hippo

median(vol.vol(ind))



On 1/12/18 10:42 AM, Helen Beaumont wrote:
> I can use mri_segstats to get mean and std dev for values within a
> segmented image. Is there any way I can get median values?
>
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Re: [Freesurfer] why freesurfer is not able to segment frontal cortex

[Douglas Greve]

Use aparc+aseg.mgz


On 1/12/18 5:14 AM, Vidhu Agrawal wrote:

Does freesurfer segments frontal cortex?

If yes the how we can do that

I have tried to do it by using the command :mri_binarize --i aseg.mgz 
--o ctx-lh-s_frontal_superior.nii --match 1156

mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154
mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_middle.nii --match 1156
mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_operacula.nii 
--match 1106
mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_orbital.nii --match 
1107
mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_triangula.nii 
--match 1108

mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_middle.nii --match 1109
mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_superior.nii --match 1110


but it is not segmenting any region

Looking forward for your reply.

Thanking you
With regards
vidhu agarwal



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Re: [Freesurfer] Visualisation left and right hemisphere

[Douglas Greve]

Hi Ahmad, you can use mris_left_right_register to register the left and 
right hemis, then mris_apply_reg to map the left annot to the right (or 
other way around).


ps. please remember to post to the FS list. Thanks!


On 1/17/18 9:13 AM, Ahmad Mheich wrote:

/Hello, /
//
/Is it possible to combine the lh and rh annotation files into a 
single //annotation file for visualisation? How? /

/Best regards/
/Ahmad/


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Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

[Carissa Nicole Weis]

I've uploaded the data. Just want to confirm you received it.

Thanks,

Carissa

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Saturday, January 13, 2018 3:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?


Those are pretty standard dimensions, so memory is not likely to be a problem. 
Can you upload a zip file with this subject's entire TRACULA subject dir for me 
here: https://gate.nmr.mgh.harvard.edu/filedrop2/


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Carissa Nicole Weis >
Sent: Saturday, January 13, 2018 10:14:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?


How much memory would you recommend using? I've been using 8gb from our cluster 
for each step in TRACULA.



The diffusion images were acquired with fairly common parameters: 3 B=0 images, 
35 different gradient directions at B=800 with 70 slices per direction at a 
voxel size of 2x2x2mm for a 128x128 matrix.



Thanks for your help!



Carissa



From: 
>
 on behalf of "Yendiki, Anastasia" 
>
Reply-To: Freesurfer support list 
>
Date: Friday, January 12, 2018 at 2:15 PM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?



Hi Carissa - One possibility is that you may be running out of memory. What are 
the dimensions of your diffusion images?



a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Carissa Nicole Weis >
Sent: Thursday, January 11, 2018 4:55:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?



Hello Anastasia!



I've since tried to rerun -bedp with this same subject and the output still did 
not indicate it had completed.



Thanks for your help!



Carissa



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Thursday, January 11, 2018 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?



Hi Carissa - It loks like bedpost ran fine. Can you please attach your entire 
log file (scripts/trac-all.log)? It's hard to tell what went wrong just from 
the end of it.



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Carissa Nicole Weis >
Sent: Tuesday, January 9, 2018 11:42:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?



Hello all,



I've been running trac-all from the command line without the configuration file 
since I'm not changing any defaults. I've successfully run several subjects 
through the trac-all -prep stage, and the -bedp stage. **Although I never got 
the "trac-all -bedp finished without error" prompt in the -bedp terminal output 
and usually just get something that says at the end:



../freesurfer_6.0/bin/bedpost_mgh: line 440: 46773 Terminated   
${subjdir}.bedpostX/monitor



OR it'll make it to something like...



37 slices processed

38 slices processed

Queuing post processing stage

46 slices processed



...and that's as far as the output in the terminal goes.



It appears all the expected files have been created in dmri.bedpostx/ so I was 
assuming this step had been completed. However, when I go to run the -paths 
step I get an error that says:



Loading DWIs from 
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/dmri/dwi.nii.gz

Loading mask from 
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dlabel/diff/aparc+aseg_mask.bbr.nii.gz

Loading BEDPOST parameter samples from 

Re: [Freesurfer] mri_em_register and mri_ca_register

[Ricardo Valle]

I see. Thank you very much!
Cheers,
Ruy
> On Jan 18, 2018, at 1:24 PM, Bruce Fischl  wrote:
> 
> Hi Ruy
> 
> they both register to a .gca atlas that is quite a bit more accurate than 
> the MNI. The details are in the 2002 and 2004 papers.
> 
> cheers
> Bruce
> On Thu, 18 Jan 2018, 
> Ricardo Valle wrote:
> 
>> Dear Freesurfer community,
>> 
>> I would like to get a better sense of how mri_em_register and 
>> mri_ca_register work. I understand the former is a linear registration and 
>> the latter is nonlinear, and that they are both meant to register an 
>> individual to a template space (MNI152?).
>> 
>> Would it be possible to update the wiki pages to give more information about 
>> the algorithms and cost functions used and other such details? And to 
>> provide references to the literature in support of the algorithms if 
>> possible?
>> 
>> Thank you. Best regards,
>> Ruy
>> ___
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>> 
>> 
>> 
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Re: [Freesurfer] mri_em_register and mri_ca_register

[Bruce Fischl]

Hi Ruy

they both register to a .gca atlas that is quite a bit more accurate than 
the MNI. The details are in the 2002 and 2004 papers.

cheers
Bruce
On Thu, 18 Jan 2018, 
Ricardo Valle wrote:

> Dear Freesurfer community,
>
> I would like to get a better sense of how mri_em_register and mri_ca_register 
> work. I understand the former is a linear registration and the latter is 
> nonlinear, and that they are both meant to register an individual to a 
> template space (MNI152?).
>
> Would it be possible to update the wiki pages to give more information about 
> the algorithms and cost functions used and other such details? And to provide 
> references to the literature in support of the algorithms if possible?
>
> Thank you. Best regards,
> Ruy
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi Andrew

Thank you for your response. I gave it a go and still no luck, unless I am
missing something completely obvious here

trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> quote PASV
227 Entering Passive Mode (132,183,202,158,147,251).
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.





On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
wrote:

> Hi Trisanna,
>
> Try running 'quote PASV' in ftp before running 'put' - that should
> hopefully clear up this issue.
>
> best,
> Andrew
>
>
> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Sorry, Bruce. ignore my last email. Not sure what happened there.
>
> I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
> get the following and it happens over and over. Any idea what the problem
> could be?
>
> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> put icbm-205.tar.gz
> local: icbm-205.tar.gz remote: icbm-205.tar.gz
> 200 PORT command successful. Consider using PASV.
> 425 Failed to establish connection.
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>> Thanks Bruce. I have uploaded it but I would like to confirm that you
>> received the ICBM_305.tar. For some reason I was not able to compress it
>> any further.
>>
>> To clarify, subjects 205 and now subject 202 have both failed after
>> surface extraction.
>>
>> best
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl > > wrote:
>>
>>> you can put it on our ftp site:
>>>
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>>> On Tue, 16 Jan
>>> 2018, Trisanna Sprung-Much
>>> wrote:
>>>
>>> > Hi Bruce
>>> > Thanks for the speedy reply. Should I attach it here or is there a
>>> place I can upload it to?
>>> >
>>> > best
>>> > Trisanna
>>> >
>>> > --
>>> > Ph.D. CandidateMcGill University
>>> > Integrated Program in Neuroscience
>>> > Psychology
>>> >
>>> >
>>> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> >   hmmm, I've never seen 

[Freesurfer] mri_em_register and mri_ca_register

[Ricardo Valle]

Dear Freesurfer community,

I would like to get a better sense of how mri_em_register and mri_ca_register 
work. I understand the former is a linear registration and the latter is 
nonlinear, and that they are both meant to register an individual to a template 
space (MNI152?). 

Would it be possible to update the wiki pages to give more information about 
the algorithms and cost functions used and other such details? And to provide 
references to the literature in support of the algorithms if possible?

Thank you. Best regards,
Ruy
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Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

[Bruce Fischl]

Hi Mohamed

if you tar, gzip and ftp this subject to our ftp site we will take a look
cheers
Bruce
On 
Thu, 18 Jan 2018, m.ba...@uliege.be wrote:



Dear Bruce,

Attached is the screen shot of the results of the segmentation of the 
perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi 
does not cover the entire cortical thickness of the region. Is there any other 
alternative to get a better segmentation of this region?

Many thanks in advance,

Best regards,

Mohamed

- Mail original -
De: "Bruce Fischl" 
À: "Freesurfer support list" 
Envoyé: Mardi 9 Janvier 2018 14:50:16
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

I'm pretty sure this was an issue with the ribbon-filling in V5 that is
better in V6. Try using it and see if it is fixed.

cheers
Bruce
On Tue, 9 Jan 2018,
m.ba...@uliege.be wrote:


Dear Freesurfer experts,

We would like to use volume and cortical thickness measures obtained for the 
perirhinal cortex in Freesurfer 5. When checking the region that has been 
segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem 
to cover the entire cortical thickness of the region. On the coronal slice 
shown in example (attached file), one can see that there are still a few voxels 
of gray matter between the external border of the ROI and the external boundary 
of the cortex. How reliable is this segmentation? Is there a reason why the ROI 
appears so thin?

Many thanks in advance,

Best regards,




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[Freesurfer] motion parameter in preprocessing stream

[Carme Uribe Codesal]

Dear all FreeSurfer users,

I was wondering if I can extract any parameter of movement from the
recon-all processing using FreeSurfer 5.1.

Thanks in advance!

Kind regards,

Carme
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[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

[Renew Andrade]

Hello:
I run the command to open freeview -v…(the installation guide example in Bert) 
and I get the error in I point out in the subject of this email. Thanks for the 
help in advance!
Sincerely,
Rene Andrade. 


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[Freesurfer] Freesurfer longitudinal templates failed - time points from different scanners

[Ambrosino di Bruttopilo-3, S.]

Dear  experts,

I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired with 
identical protocol (ADNI) but 2 different Philips 3T scanners (all time 1 with 
Achieva, all time 2 with Ingenia). Unfortunately ~ 50% of the within-subjects 
templates completely failed. Is there anything I could try to fix this, or 
should just accept that is not possible to run FS longitudinal with this data?

Thanks a lot!

Sara

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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

[M del Mar Velasco]

Hi Andrew,

My test in December with last version of make_average_surface worked correctly.

However, now I am trying to make another average subject and medial_wall.label 
is not created. I am using the last patch as last time. It is unusual because 
last time label folder was correctly created. I have realized mri_aparc2aseg is 
not working fine because I get an error log. I've attached it. I can send you 
to our ftp server whole average subject folder if you consider it appropiate.

Many thanks,


Cheers,


M del Mar


error.log
Description: error.log


recon-all.log
Description: recon-all.log
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