[Freesurfer] Left & Right flip on asymmetric MNI template

[yskim]

 
 
  Dear Freesurfer experts,I recently received manually segmentated MR data that 
registered to ch2better MNI template.

  
  However, I have been informed that this data has been registered in inverted 
form, and I could not simply flip left and right because ch2better MNI template 
was asymmetric.To solve this problem, I first used the LeftRightReversal method 
of freesurfer, but this method did not properly reflect the left-right 
different structure of the asymmetric template.How can I flip registered data 
successfully with reflecting asymmetric MNI template structure?
  
  Thank you for your help and information.

- yskim
   
  
 
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Re: [Freesurfer] FS-FAST longitudinal analyis

[Douglas Greve]

That looks correct. You can also checkout the instructions here:

https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis


On 9/17/17 6:07 PM, std...@virgilio.it wrote:

Hi list,

I'm not sure that the files reported below are correct to assess the 
longitudinal difference between T1 and T2.
Please, could you check it? The result which I have obtained bu 
running mri_glmfit is too strange.

Thanks
Best regards
Stefano

1) PAIRWISE.fsgd file
---
GroupDescriptorFile 1
Class subj1
Class subj2
...
Class subjN
Variables TP1-vs-TP2
Input subj1_tp1 subj1 1
Input subj1_tp2 subj1 -1
Input subj2_tp1 subj2 1
Input subj2_tp2 subj2 -1
...
Input subjN_tp1 subjN 1
Input subjN_tp2 subjN -1


2) mean.mtx
1 1 ... 1 0
--
3) tp-effect.mtx
0 0 ... 0 1
--
4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz --wls cesvar.nii.gz 
--surface fsaverage rh --nii.gz --fsgd PAIRWISE.fsgd doss --C mean.mtx 
--C tp-effect.mtx



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Re: [Freesurfer] Fw: Multiple comparison, color maps and contrast

[Douglas Greve]

On 9/17/17 5:26 PM, miracle ozzoude wrote:



Sent from my BlackBerry 10 smartphone.
*From: *miracle ozzoude 
*Sent: *Sunday, September 17, 2017 11:01 AM
*To: *Freesurfer support list
*Subject: *Multiple comparison, color maps and contrast


Hello,

I want to run a whole brain cortical thickness analysis and I will 
like to confirm some steps.
a) for correcting for multiple comparison, I want to use both Monte 
Carlo and permutations in order to compare the difference. Are these 
the right commands?
 Monte Carlo : mri_glmfit-sim --glmdir lh.name.glmdir --sim mc-z 5000 
2 mc-z.abs.2 --sm-sign abs --cwp 0.05 --overwrite
That looks correct, but you don't need to run it unless you are not 
doing a whole hemisphere correction.
 Permutation: mri_glmfit-sim --glmdir lh.name.glmdir --sim perm 5000 2 
 permcsd --sim-sign abs --cwp 0.05 --perm-resid --overwrite
That is correct, though you may want to name the csd something more 
meaningful like perm.abs.2


b) I have 2 groups and a contrast of (1 -1 0 0) representing where 
group 1> group 2 removing the effect of age. If I correct for multiple 
comparisons using abs and while visualizing my result the color map 
for the surviving clusters is blue , this means areas where  group 1 < 
group 2. If the color map for the surviving clusters is red/yellow, 
this means areas where group 1> group 2.

correct


Thank you.
Best,
Paul


Sent from my BlackBerry 10 smartphone.






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Re: [Freesurfer] labels used by freesurfer

[Douglas Greve]

Can you post the numbers for each item? Your first calculation is over 
200 thousand mm3 (10x the 2nd calc) which suggests a math error



On 9/17/17 2:55 PM, Benjamin Luerweg wrote:

alright.. so far…BUT:

Ive tried to get the volume of the ventricle system by using two 
different calculations.


first of all i tried to get the volume by: brainsegvol - 
brainsegvolnotvent
than i tried to simply add all the seprate parts of the ventricle 
system (rh lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle)


after doing this i realized that the two values were differing like -> 
217820,00 (first calculation) and 20115,8998 (second calculation)

any ideas why the difference is that big?


kind regards



Am 17.09.2017 um 20:51 schrieb Bruce Fischl 
>:


yes, you can add the various components of the cc or cingulate to get 
total volume


As for the CSF label, I think it's for bits of csf that can be seen 
or inferred on a T1 in sulci and maybe inferior regions. You might 
want to check the original CMA (Caviness, Kenndy, et al) papers, but 
I imagine it's small enough that it doesn't matter much. I believe it 
is *not* part of the ventricular system


On Sun, 17 Sep 2017, Benjamin Luerweg wrote:


hey mr greve,
hey fs community,

what do you think about adding the volumes of seperated parts of one 
structure to a complete volume?

e.g. the corpus callosum or also cingulate gyrus.

is it ok to get the complete volume value by just adding the volumes 
of the seperated parts?


beside that, am i right that wmparc parts of e.g. insula is just the 
white matter volume?
would it be ok to add the volume of the aparc equivalent as the grey 
matter volume part?



i really tried to find out what the label CSF stands for.. but 
beside realizing that its not a common/regular part of the ventricle 
system
i couldn’t get any other informations regarding the meaning? of the 
CSF label.


i tried to find out whats it about by using freeview (screenshot 
(black part))

anyone any idea?



kind regards,
ben






Am 14.09.2017 um 20:56 schrieb Benjamin Luerweg 
>:


thx so far! really thank you.. do you know how to find out more 
about that label?
what do you think about how to get any informations about a 
possible adding of different structure parts to a „complete one“ 
for example the Corpus callosum thing?


greets bl

Am 14.09.2017 um 18:40 schrieb Douglas N Greve 
>:




On 09/13/2017 05:38 PM, Benjamin Luerweg wrote:

dear mr. greve,
dear fs community,



*REGARDING CSF and CSFVol:*

i still don’t understand the whole CSF and CSFVol thing.
it seems to be impossible that CSFVol ist the volume of the CSF label
because CSFVol is *bigger* than CSF.
additional to this aspect the value of the CSF label is a volume 
itself.

They are both index 24. the "CSF" value in aseg.stats has been partial
volume corrected, so it is a little different than "CSFVol", which is
just a count of the voxels.


so my questions again:what is the label CSF (aseg.stats) describing?
and what does it stands for? cer.spinal.fluid?
what is the label CSFVol (console) describing? and what does it 
stands

for if the CSF label is a volume already?


I’ve been trying to understand the meaning of the CSF (index24) by
using freeviewer.. but no chance… for me it seems to be not part of
the ventricle system as i know it? maybe you can describe it using an
image?
Not sure. This was a label supplied to us by the center for 
morphometric

analysis (CMA) about 20 years ago, and I can't find the docs on it. It
does not appear to be part of the ventricular system. I think it 
must be

some kind of of sulcal csf in the midline. I don't know why the CMA
decided to label that and not other sulcal CSF. It is pretty small and
probably will not affect your calculations that much either way


beside that: whats the advantage of this two lables beside 
getting the
whole ventricle volume by adding ventricles (lateral,inferior 
lateral,

3rd, 4th, 5th)?

I don't understand what you mean.




*REGARDING CC (corpus callosum):*

why do you think that the corpus callosum is not a 3D body? of cause
it is or what did you mean?
setting the CC parts in free viewer it seems as if it shouldn’t be a
big deal to add the separated parts of the CC to one value?!





kind regards,
benjamin luerweg


doctoral student





Am 13.09.2017 um 00:46 schrieb Douglas N Greve
>>:


CSFVol is actually the volume of the CSF label (index 24)

3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus 
the CSF

label

VentChorVol is the volume of choroird plexus, lateral 
ventricles, and

[Freesurfer] FS-FAST longitudinal analyis

[stdp82]

Hi list,
I'm not sure that the files reported below are correct to assess the 
longitudinal difference between T1 and T2.Please, could you check it? The 
result which I have obtained bu running mri_glmfit is too strange.ThanksBest 
regardsStefano
1) PAIRWISE.fsgd file---GroupDescriptorFile 1Class subj1Class 
subj2...Class subjNVariables TP1-vs-TP2Input subj1_tp1 subj1 1Input subj1_tp2 
subj1 -1Input subj2_tp1 subj2 1Input subj2_tp2 subj2 -1...Input subjN_tp1 subjN 
1Input subjN_tp2 subjN -1
2) mean.mtx1 1 ... 1 0--3) tp-effect.mtx0 0 ... 0 
1--4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz 
--wls cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd PAIRWISE.fsgd doss 
--C mean.mtx --C tp-effect.mtx___
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[Freesurfer] Fw: Multiple comparison, color maps and contrast

[miracle ozzoude]

  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Sunday, September 17, 2017 11:01 AMTo: Freesurfer support listSubject: Multiple comparison, color maps and contrast  Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm some steps. a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands?  Monte Carlo : mri_glmfit-sim --glmdir lh.name.glmdir --sim mc-z 5000 2 mc-z.abs.2 --sm-sign abs --cwp 0.05 --overwrite Permutation: mri_glmfit-sim --glmdir lh.name.glmdir --sim perm 5000 2  permcsd --sim-sign abs --cwp 0.05 --perm-resid --overwriteb) I have 2 groups and a contrast of (1 -1 0 0) representing where group 1> group 2 removing the effect of age. If I correct for multiple comparisons using abs and while visualizing my result the color map for the surviving clusters is blue , this means areas where  group 1 < group 2. If the color map for the surviving clusters is red/yellow, this means areas where group 1> group 2. Thank you.   Best, Paul Sent from my BlackBerry 10 smartphone.

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] labels used by freesurfer

[Benjamin Luerweg]

alright.. so far…BUT:

Ive tried to get the volume of the ventricle system by using two different 
calculations.

first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent
than i tried to simply add all the seprate parts of the ventricle system (rh 
lat ventricle + lh lat ventricle + 3rd, 4th and 5th ventricle)

after doing this i realized that the two values were differing like -> 
217820,00 (first calculation) and 20115,8998 (second calculation)
any ideas why the difference is that big?


kind regards



> Am 17.09.2017 um 20:51 schrieb Bruce Fischl :
> 
> yes, you can add the various components of the cc or cingulate to get total 
> volume
> 
> As for the CSF label, I think it's for bits of csf that can be seen or 
> inferred on a T1 in sulci and maybe inferior regions. You might want to check 
> the original CMA (Caviness, Kenndy, et al) papers, but I imagine it's small 
> enough that it doesn't matter much. I believe it is *not* part of the 
> ventricular system
> 
> On Sun, 17 Sep 2017, Benjamin Luerweg wrote:
> 
>> hey mr greve,
>> hey fs community,
>> 
>> what do you think about adding the volumes of seperated parts of one 
>> structure to a complete volume?
>> e.g. the corpus callosum or also cingulate gyrus.
>> 
>> is it ok to get the complete volume value by just adding the volumes of the 
>> seperated parts?
>> 
>> beside that, am i right that wmparc parts of e.g. insula is just the white 
>> matter volume?
>> would it be ok to add the volume of the aparc equivalent as the grey matter 
>> volume part?
>> 
>> 
>> i really tried to find out what the label CSF stands for.. but beside 
>> realizing that its not a common/regular part of the ventricle system
>> i couldn’t get any other informations regarding the meaning? of the CSF 
>> label.
>> 
>> i tried to find out whats it about by using freeview (screenshot (black 
>> part))
>> anyone any idea?
>> 
>> 
>> 
>> kind regards,
>> ben
>> 
>> 
>> 
>> 
>> 
>> 
>>> Am 14.09.2017 um 20:56 schrieb Benjamin Luerweg 
>>> :
>>> 
>>> thx so far! really thank you.. do you know how to find out more about that 
>>> label?
>>> what do you think about how to get any informations about a possible adding 
>>> of different structure parts to a „complete one“ for example the Corpus 
>>> callosum thing?
>>> 
>>> greets bl
>>> 
 Am 14.09.2017 um 18:40 schrieb Douglas N Greve >>:
 
 
 
 On 09/13/2017 05:38 PM, Benjamin Luerweg wrote:
> dear mr. greve,
> dear fs community,
> 
> 
> 
> *REGARDING CSF and CSFVol:*
> 
> i still don’t understand the whole CSF and CSFVol thing.
> it seems to be impossible that CSFVol ist the volume of the CSF label
> because CSFVol is *bigger* than CSF.
> additional to this aspect the value of the CSF label is a volume itself.
 They are both index 24. the "CSF" value in aseg.stats has been partial
 volume corrected, so it is a little different than "CSFVol", which is
 just a count of the voxels.
> 
> so my questions again:what is the label CSF (aseg.stats) describing?
> and what does it stands for? cer.spinal.fluid?
> what is the label CSFVol (console) describing? and what does it stands
> for if the CSF label is a volume already?
> 
> 
> I’ve been trying to understand the meaning of the CSF (index24) by
> using freeviewer.. but no chance… for me it seems to be not part of
> the ventricle system as i know it? maybe you can describe it using an
> image?
 Not sure. This was a label supplied to us by the center for morphometric
 analysis (CMA) about 20 years ago, and I can't find the docs on it. It
 does not appear to be part of the ventricular system. I think it must be
 some kind of of sulcal csf in the midline. I don't know why the CMA
 decided to label that and not other sulcal CSF. It is pretty small and
 probably will not affect your calculations that much either way
> 
> beside that: whats the advantage of this two lables beside getting the
> whole ventricle volume by adding ventricles (lateral,inferior lateral,
> 3rd, 4th, 5th)?
 I don't understand what you mean.
> 
> 
> 
> *REGARDING CC (corpus callosum):*
> 
> why do you think that the corpus callosum is not a 3D body? of cause
> it is or what did you mean?
> setting the CC parts in free viewer it seems as if it shouldn’t be a
> big deal to add the separated parts of the CC to one value?!
> 
> 
> 
> 
> 
> kind regards,
> benjamin luerweg
> 
> 
> doctoral student
> 
> 
> 
> 
>> Am 13.09.2017 um 00:46 schrieb Douglas N Greve
>> > 

Re: [Freesurfer] labels used by freesurfer

[Bruce Fischl]

yes, you can add the various components of the cc or cingulate to get total 
volume


As for the CSF label, I think it's for bits of csf that can be seen or 
inferred on a T1 in sulci and maybe inferior regions. You might want to 
check the original CMA (Caviness, Kenndy, et al) papers, but I imagine it's 
small enough that it doesn't matter much. I believe it is *not* part of the 
ventricular system


On Sun, 17 Sep 2017, 
Benjamin Luerweg wrote:



hey mr greve,
hey fs community,

what do you think about adding the volumes of seperated parts of one structure 
to a complete volume?
e.g. the corpus callosum or also cingulate gyrus.

is it ok to get the complete volume value by just adding the volumes of the 
seperated parts?

beside that, am i right that wmparc parts of e.g. insula is just the white 
matter volume?
would it be ok to add the volume of the aparc equivalent as the grey matter 
volume part?


i really tried to find out what the label CSF stands for.. but beside realizing 
that its not a common/regular part of the ventricle system
i couldn’t get any other informations regarding the meaning? of the CSF label.

i tried to find out whats it about by using freeview (screenshot (black part))
anyone any idea?



kind regards,
ben







Am 14.09.2017 um 20:56 schrieb Benjamin Luerweg 
:

thx so far! really thank you.. do you know how to find out more about that 
label?
what do you think about how to get any informations about a possible adding of 
different structure parts to a „complete one“ for example the Corpus callosum 
thing?

greets bl


Am 14.09.2017 um 18:40 schrieb Douglas N Greve >:



On 09/13/2017 05:38 PM, Benjamin Luerweg wrote:

dear mr. greve,
dear fs community,



*REGARDING CSF and CSFVol:*

i still don’t understand the whole CSF and CSFVol thing.
it seems to be impossible that CSFVol ist the volume of the CSF label
because CSFVol is *bigger* than CSF.
additional to this aspect the value of the CSF label is a volume itself.

They are both index 24. the "CSF" value in aseg.stats has been partial
volume corrected, so it is a little different than "CSFVol", which is
just a count of the voxels.


so my questions again:what is the label CSF (aseg.stats) describing?
and what does it stands for? cer.spinal.fluid?
what is the label CSFVol (console) describing? and what does it stands
for if the CSF label is a volume already?


I’ve been trying to understand the meaning of the CSF (index24) by
using freeviewer.. but no chance… for me it seems to be not part of
the ventricle system as i know it? maybe you can describe it using an
image?

Not sure. This was a label supplied to us by the center for morphometric
analysis (CMA) about 20 years ago, and I can't find the docs on it. It
does not appear to be part of the ventricular system. I think it must be
some kind of of sulcal csf in the midline. I don't know why the CMA
decided to label that and not other sulcal CSF. It is pretty small and
probably will not affect your calculations that much either way


beside that: whats the advantage of this two lables beside getting the
whole ventricle volume by adding ventricles (lateral,inferior lateral,
3rd, 4th, 5th)?

I don't understand what you mean.




*REGARDING CC (corpus callosum):*

why do you think that the corpus callosum is not a 3D body? of cause
it is or what did you mean?
setting the CC parts in free viewer it seems as if it shouldn’t be a
big deal to add the separated parts of the CC to one value?!





kind regards,
benjamin luerweg


doctoral student





Am 13.09.2017 um 00:46 schrieb Douglas N Greve
>>:

CSFVol is actually the volume of the CSF label (index 24)

3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF
label

VentChorVol is the volume of choroird plexus, lateral ventricles, and
inferior lateral ventricles

 BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ;



On 09/12/2017 02:13 PM, Benjamin Luerweg wrote:

Hey Mr. Greve,

thank your very much again!
if i understand you right, the inside the console shown up values
can’t be extracted into a separate file?

beside that, this values are of interest for me, so that i copied them
to a text file.
as you can see:Getting Brain Volume Statistics
...
SubCortGMVol 56306.000
SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343
SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352
BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231
BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034
BrainSegVolNotVent 1082437.000
CerebellumVol 145310.000
VentChorVol   23535.000
3rd4th5thCSF   3528.000
CSFVol   963.000,
OptChiasmVol   154.000
MaskVol 1526326.000

am i right that this CSFVol is the Volume of all ventricles not

Re: [Freesurfer] labels used by freesurfer

[Benjamin Luerweg]

hey mr greve,
hey fs community,

what do you think about adding the volumes of seperated parts of one structure 
to a complete volume?
e.g. the corpus callosum or also cingulate gyrus. 

is it ok to get the complete volume value by just adding the volumes of the 
seperated parts? 

beside that, am i right that wmparc parts of e.g. insula is just the white 
matter volume?
would it be ok to add the volume of the aparc equivalent as the grey matter 
volume part?


i really tried to find out what the label CSF stands for.. but beside realizing 
that its not a common/regular part of the ventricle system 
i couldn’t get any other informations regarding the meaning? of the CSF label.

i tried to find out whats it about by using freeview (screenshot (black part))
anyone any idea?



kind regards,
ben






> Am 14.09.2017 um 20:56 schrieb Benjamin Luerweg 
> :
> 
> thx so far! really thank you.. do you know how to find out more about that 
> label?
> what do you think about how to get any informations about a possible adding 
> of different structure parts to a „complete one“ for example the Corpus 
> callosum thing?
> 
> greets bl
> 
>> Am 14.09.2017 um 18:40 schrieb Douglas N Greve > >:
>> 
>> 
>> 
>> On 09/13/2017 05:38 PM, Benjamin Luerweg wrote:
>>> dear mr. greve,
>>> dear fs community,
>>> 
>>> 
>>> 
>>> *REGARDING CSF and CSFVol:*
>>> 
>>> i still don’t understand the whole CSF and CSFVol thing.
>>> it seems to be impossible that CSFVol ist the volume of the CSF label 
>>> because CSFVol is *bigger* than CSF.
>>> additional to this aspect the value of the CSF label is a volume itself.
>> They are both index 24. the "CSF" value in aseg.stats has been partial 
>> volume corrected, so it is a little different than "CSFVol", which is 
>> just a count of the voxels.
>>> 
>>> so my questions again:what is the label CSF (aseg.stats) describing? 
>>> and what does it stands for? cer.spinal.fluid?
>>> what is the label CSFVol (console) describing? and what does it stands 
>>> for if the CSF label is a volume already?
>>> 
>>> 
>>> I’ve been trying to understand the meaning of the CSF (index24) by 
>>> using freeviewer.. but no chance… for me it seems to be not part of 
>>> the ventricle system as i know it? maybe you can describe it using an 
>>> image?
>> Not sure. This was a label supplied to us by the center for morphometric 
>> analysis (CMA) about 20 years ago, and I can't find the docs on it. It 
>> does not appear to be part of the ventricular system. I think it must be 
>> some kind of of sulcal csf in the midline. I don't know why the CMA 
>> decided to label that and not other sulcal CSF. It is pretty small and 
>> probably will not affect your calculations that much either way
>>> 
>>> beside that: whats the advantage of this two lables beside getting the 
>>> whole ventricle volume by adding ventricles (lateral,inferior lateral, 
>>> 3rd, 4th, 5th)?
>> I don't understand what you mean.
>>> 
>>> 
>>> 
>>> *REGARDING CC (corpus callosum):*
>>> 
>>> why do you think that the corpus callosum is not a 3D body? of cause 
>>> it is or what did you mean?
>>> setting the CC parts in free viewer it seems as if it shouldn’t be a 
>>> big deal to add the separated parts of the CC to one value?!
>>> 
>>> 
>>> 
>>> 
>>> 
>>> kind regards,
>>> benjamin luerweg
>>> 
>>> 
>>> doctoral student
>>> 
>>> 
>>> 
>>> 
 Am 13.09.2017 um 00:46 schrieb Douglas N Greve 
 >>:
 
 CSFVol is actually the volume of the CSF label (index 24)
 
 3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF
 label
 
 VentChorVol is the volume of choroird plexus, lateral ventricles, and
 inferior lateral ventricles
 
  BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ;
 
 
 
 On 09/12/2017 02:13 PM, Benjamin Luerweg wrote:
> Hey Mr. Greve,
> 
> thank your very much again!
> if i understand you right, the inside the console shown up values
> can’t be extracted into a separate file?
> 
> beside that, this values are of interest for me, so that i copied them
> to a text file.
> as you can see:Getting Brain Volume Statistics
> ...
> SubCortGMVol 56306.000
> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343
> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352
> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231
> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034
> BrainSegVolNotVent 1082437.000
> CerebellumVol 145310.000
> VentChorVol   23535.000
> 3rd4th5thCSF   3528.000
> CSFVol   963.000,
> OptChiasmVol   154.000
> MaskVol 1526326.000
> 
> am i right that 

Re: [Freesurfer] longitudinal freesurfer- different scanners

[Martijn Steenwijk]

The longitudinal pipeline will not overcome (contrast) differences due to 
scanner differences. If you register the scans to eachother you will see that 
there are slight differences in WM/GM contrast. Probably better to use the 
scans from the same scanner and not use the third. 

 

 

 

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Michelle VanTieghem
Verzonden: zondag 17 september 2017 19:18
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] longitudinal freesurfer- different scanners

 

Hi all, 

 

I just wanted to follow up on my question: 

Would it be ok to use the longitudinal pipeline for scans that were acquired on 
different scanners (e.g time 1 and time 2 on the same scanner, time 3 on 
different scanner)? Would the longitudinal pipeline help to account for 
different scanners, since it creates the average base image for all 3 time 
points? or is this not recommended to use different scanners in longitudinal 
pipeline?

 

Thanks!

- M

 

On Mon, Sep 4, 2017 at 5:27 PM, Michelle VanTieghem 
 wrote:

Hello, 

 

Would it be ok to use the longitudinal pipeline for scans that were acquired on 
different scanners (e.g time 1 and time 2 on the same scanner, time 3 on 
different scanner)? Would the longitudinal pipeline help to account for 
different scanners, since it creates the average base image for all 3 time 
points? or is this not recommended?

 

Thank you,

Michelle 

 

-- 

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University 

mrv2...@columbia.edu





 

-- 

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University 

mrv2...@columbia.edu

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Re: [Freesurfer] longitudinal freesurfer- different scanners

[Michelle VanTieghem]

Hi all,

I just wanted to follow up on my question:
Would it be ok to use the longitudinal pipeline for scans that were
acquired on different scanners (e.g time 1 and time 2 on the same scanner,
time 3 on different scanner)? Would the longitudinal pipeline help to
account for different scanners, since it creates the average base image for
all 3 time points? or is this not recommended to use different scanners in
longitudinal pipeline?

Thanks!
- M

On Mon, Sep 4, 2017 at 5:27 PM, Michelle VanTieghem <
michelle.vantieg...@gmail.com> wrote:

> Hello,
>
> Would it be ok to use the longitudinal pipeline for scans that were
> acquired on different scanners (e.g time 1 and time 2 on the same scanner,
> time 3 on different scanner)? Would the longitudinal pipeline help to
> account for different scanners, since it creates the average base image for
> all 3 time points? or is this not recommended?
>
> Thank you,
> Michelle
>
> --
> Michelle VanTieghem
> PhD student in Psychology
> Developmental Affective Neuroscience Lab
> Columbia University
> mrv2...@columbia.edu
>



-- 
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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[Freesurfer] Multiple comparison, color maps and contrast

[miracle ozzoude]

 Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm some steps. a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands?  Monte Carlo : mri_glmfit-sim --glmdir lh.name.glmdir --sim mc-z 5000 2 mc-z.abs.2 --sm-sign abs --cwp 0.05 --overwrite Permutation: mri_glmfit-sim --glmdir lh.name.glmdir --sim perm 5000 2  permcsd --sim-sign abs --cwp 0.05 --perm-resid --overwriteb) I have 2 groups and a contrast of (1 -1 0 0) representing where group 1> group 2 removing the effect of age. If I correct for multiple comparisons using abs and while visualizing my result the color map for the surviving clusters is blue , this means areas where  group 1 < group 2. If the color map for the surviving clusters is red/yellow, this means areas where group 1> group 2. Thank you.   Best, Paul Sent from my BlackBerry 10 smartphone.
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Re: [Freesurfer] Hippocampal subfield segmentation error

[Md. Mamun Al-Amin]

Hi Eugenio
Thanks for your attention.
I solved this problem today. I found two JAVA versions in my macbook
(Library/Java/JavaVirtualMachines). I think they were conflicting. So I
deleted latest java folder.

By the way, I have been trying to gather the volume analyzed from all
subjects. However, it is not working.
I used following command

*quantifyHAsubregions.sh amygNuc T1 amyg.txt /Volumes/mamun/CB_Long/*

However I found nothing in my CB_Long directory.

Would you please help me solving this issue?



On Sun, Sep 17, 2017 at 7:26 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Dear MMAA,
>
> That looks like a runtime error. Did you have any problems with version
> 6.0?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of "Md. Mamun
> Al-Amin" 
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, 15 September 2017 at 00:54
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Hippocampal subfield segmentation error
>
>
>
> Dear Experts
>
> I have been experiencing a problem while running the following command
>
>
>
> *segmentHA_T1.sh subject_name*
>
> The program exits with the following error
>
>
>
> "MATLAB is exiting because of fatal error
> /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
> line 39:   660 Killed: 9   "${exe_dir}"/segmentSubjectT1_
> autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
> $args"
>
> The log file is attached herewith.
>
> I have reinstalled Matlab R2012 runtime. However, still I am experiencing
> same problem.
>
>
> Looking for a solution.
>
> I would appreciate your suggestion.
>
>
>
> --
>
>
>
> Kind regards
>
>
>
> Md. Mamun Al-Amin
>
> --
>
> PhD Candidate, Queensland Brain Institute
>
> Building 79, St Lucia QLD 4072
>
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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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> 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.
>
>


-- 

Kind regards

Md. Mamun Al-Amin
--
PhD Candidate, Queensland Brain Institute
Building 79, St Lucia QLD 4072
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