Re: [Freesurfer] error report - talairach.m3z not found

[Ramesh Babu]

Thank you Bruce

On Thu, Jun 22, 2017 at 12:45 AM, Bruce Fischl 
wrote:

> sounds like more in the graphics  card, or just reduce the number of
> simultaneous jobs
>
> On Wed, 21 Jun 2017, Ramesh Babu wrote:
>
> Dear Douglas Greve and Bruce,
>>
>> Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should
>> I increase memory of both or only graphic card?
>>
>> Thanks
>> Ramesh
>>
>> On Tue, Jun 20, 2017 at 9:02 PM, Bruce Fischl 
>> wrote:
>>   or don't run so many at the same time
>>
>>   cheers
>>   Bruce
>>   On Tue, 20 Jun 2017, Douglas Greve
>>   wrote:
>>
>>   >
>>   > The error was earlier:
>>   >
>>   > CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of
>> memory.
>>   > Abort (core dumped)
>>   > ERROR: mri_ca_register with non-zero status 134
>>   >
>>   > looks like you need more memory in your gpu
>>   >
>>   > On 6/20/17 7:30 AM, Ramesh Babu wrote:
>>   >   Dear Expert,
>>   >
>>   > The recon-all -all process has stopped abruptly and error report
>> shows
>>   > that "cannot find or read transforms/talairach.m3z". Please see
>> the
>>   > attached file. Processing was running in 5 terminal
>> simultaneously and
>>   > it has happened for two processing. Others exited without error.
>> Could
>>   > please tell what should I do to continue the interrupted one.
>>   >
>>   > Thanks in advance
>>   > Ramesh
>>   >
>>   >
>>   > ___
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>>   > Freesurfer@nmr.mgh.harvard.edu
>>   > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>   >
>>   >
>>   >
>>   >
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>>
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>>
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Re: [Freesurfer] DKT vs. DK Freesurfer atlases

[Bruce Fischl]

Hi Gabor,

I'm not sure it is identical, but it should be pretty close

cheers
Bruce
On Wed, 21 Jun 
2017, Gabor Perlaki wrote:



Dear all,

Could anybody help me with the below questions please?

  Dear all,


I've found an article comparing DK and DKT atlas based automatic
segmentations to manual labels (Klein and Tourville, Front Neurosci.
2012; 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/).
It seems that using DKT40 works better than DK in most of the cortical
regions (based on Dice).
Does anybody know that the DKTatlas related results created by
Freesurfer (e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are
based on the same DKT40 atlas used in the article and whether the
DKT40 atlas related results were also created by Freesurfer in the
article by Klein and Tourville? Are the Freesurfer created results in
lh.aparc.DKTatlas.stats generally more reliable than the results in
lh.aparc.stats?



--
Gabor Perlaki
research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-30-2084367
E-mail: petzinger.ga...@gmail.com



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Re: [Freesurfer] TRACULA -prep ERROR

[Z K]

Hello Maria,

This is a known issue with a freesurfer v6 script and more recent 
versions of macOS. Can you please source freesurfer and then issue the 
following command:

   sudo -E fs_update

Its should update your installation and resolve the issue.




On 06/21/2017 11:43 AM, Maria Economou wrote:
> Dear Freesurfer community,
> 
> I'm having trouble completing the pre-processing step for TRACULA analysis.
> I'm using a single NifTi file which I've converted using the original 
> DICOMS, acquired by a PHILIPS scanner. However, I get the following 
> errors in the command line:
> 
> 
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>Referenced from: 
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>Expected in: /usr/lib/libSystem.B.dylib
> 
> dyld: Symbol not found: ___emutls_get_address
>Referenced from: 
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>Expected in: /usr/lib/libSystem.B.dylib
> 
> Trace/BPT trap
> ERROR: input file must be in NIfTI format
> Darwin dyn143100.shef.ac.uk  15.6.0 Darwin 
> Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; 
> root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64
> 
> trac-preproc exited with ERRORS at Wed Jun 21 16:22:34 BST 2017
> 
> 
> I double-checked my configuration file and everything (bvals and bvecs) 
> looks like is formatted appropriately. I also tried running the command 
> with -i and -s flags, but i get the same errors.
> Please find attached below the trac-all.log
> 
> I would really appreciate any advice as to why it's not working and what 
> I might be doing wrong!
> 
> Many thanks,
> Maria.
> 
> 
> 
> 
> 
> 
> ___
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Re: [Freesurfer] Surface Problem

[Z K]

Can you send me your recon-all script to my email address (not to the 
list). I suspect it has been modified.

On 06/21/2017 02:04 PM, Michael Davies wrote:
> Hello, i have been trying to regenerate the surface on one of my 
> subjects but keep having a problem where the terminal is saying there is 
> a missing file name. Do you have any suggestions please?
> 
> 
> Kind regards, Michael
> 
> 
> bash-4.1$ freesurfer_setup_freeview
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR   /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj5/Subj5
> bash-4.1$ recon-all -autorecon-pial -s Subj5
> if: Missing file name.
> bash-4.1$
> 
> 
> 
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Re: [Freesurfer] DKT vs. DK Freesurfer atlases

[Gabor Perlaki]

Dear all,

Could anybody help me with the below questions please?

Dear all,
>
>
> I've found an article comparing DK and DKT atlas based automatic
> segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012;
> 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/). It seems
> that using DKT40 works better than DK in most of the cortical regions
> (based on Dice).
> Does anybody know that the DKTatlas related results created by Freesurfer
> (e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the
> same DKT40 atlas used in the article and whether the DKT40 atlas related
> results were also created by Freesurfer in the article by Klein and
> Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats
> generally more reliable than the results in lh.aparc.stats?
>
>
>
> --
> Gabor Perlaki
> research associate
> Diagnostic Center of Pécs
> H-7623 Pécs, Rét str. 2.
> Tel.: 0036-30-2084367
> E-mail: petzinger.ga...@gmail.com
>


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Re: [Freesurfer] error report - talairach.m3z not found

[Bruce Fischl]

sounds like more in the graphics  card, or just reduce the number of 
simultaneous jobs

On Wed, 21 Jun 2017, Ramesh Babu wrote:


Dear Douglas Greve and Bruce,

Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should I 
increase memory of both or only graphic card?

Thanks
Ramesh

On Tue, Jun 20, 2017 at 9:02 PM, Bruce Fischl  
wrote:
  or don't run so many at the same time

  cheers
  Bruce
  On Tue, 20 Jun 2017, Douglas Greve
  wrote:

  >
  > The error was earlier:
  >
  > CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of 
memory.
  > Abort (core dumped)
  > ERROR: mri_ca_register with non-zero status 134
  >
  > looks like you need more memory in your gpu
  >
  > On 6/20/17 7:30 AM, Ramesh Babu wrote:
  >       Dear Expert,
  >
  > The recon-all -all process has stopped abruptly and error report shows
  > that "cannot find or read transforms/talairach.m3z". Please see the
  > attached file. Processing was running in 5 terminal simultaneously and
  > it has happened for two processing. Others exited without error. Could
  > please tell what should I do to continue the interrupted one.
  >
  > Thanks in advance
  > Ramesh
  >
  >
  > ___
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  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >
  >
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Re: [Freesurfer] TRACULA -prep ERROR

[Yendiki, Anastasia]

Hi Maria – Can you please run the mri_info command on the same nifti volume on 
the same computer and let us know what the output is?

a.y

From: 
>
 on behalf of Maria Economou 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, June 21, 2017 at 11:43 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] TRACULA -prep ERROR

Dear Freesurfer community,

I'm having trouble completing the pre-processing step for TRACULA analysis.
I'm using a single NifTi file which I've converted using the original DICOMS, 
acquired by a PHILIPS scanner. However, I get the following errors in the 
command line:


dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap
ERROR: input file must be in NIfTI format
Darwin dyn143100.shef.ac.uk 15.6.0 Darwin Kernel 
Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; 
root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Wed Jun 21 16:22:34 BST 2017


I double-checked my configuration file and everything (bvals and bvecs) looks 
like is formatted appropriately. I also tried running the command with -i and 
-s flags, but i get the same errors.
Please find attached below the trac-all.log

I would really appreciate any advice as to why it's not working and what I 
might be doing wrong!

Many thanks,
Maria.




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[Freesurfer] Surface Problem

[Michael Davies]

Hello, i have been trying to regenerate the surface on one of my subjects but 
keep having a problem where the terminal is saying there is a missing file 
name. Do you have any suggestions please?


Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj5/Subj5
bash-4.1$ recon-all -autorecon-pial -s Subj5
if: Missing file name.
bash-4.1$

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Re: [Freesurfer] Segmentation problem recon-all

[Bruce Fischl]

Hi Marine

the brainmask is just a rough estimate of what is brain and what is not. 
You don't need to worry if it is not accurate *unless* the lh.pial and/or 
rh.pial surfaces end up not being accurate because of dura left in the 
brainmask.


cheers
Bruce
On Wed, 21 Jun 2017, Lisa Delalande wrote:



Hi,

 

I am a PhD student and faced a problem with Freesurfer, more specially with
segmentation. First of all, I did a typical qsub command. However, when I
cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are
often considered as grey matter.

I tried these different commands :


1.) setenv SUBJECTS_DIR /path/to/your/data

setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50'

recon-all -multistrip -clean-bm -s  -no-isrunning


2.) recon-all -skullstrip -clean-bm -gcut -subjid 

cd $SUBJECTS_DIR/yoursubj/mri/transforms

cp talairach_with_skull.lta bak

cp talairach_with_skull_2.lta talairach_with_skull.lta

recon-all -s yoursubj -skullstrip -clean-bm -clean-lta"

 

without success I finally used a manual method :

 

3.) tkmedit skullstrip3_before brainmask.mgz -aux T1.mgz

 

but the latter is source of error and time-consuming. I've got 105 MRI scans
to rectify. Do you have a council to improve le first step of the reconn-all
?


Sincerely
Marine Moyon


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Re: [Freesurfer] Freesurfer with infarct patients

[Bruce Fischl]

Hi Mariana

yes, control points would mess everything up. It looks like the rest of the 
surface was generated pretty accurately though - do you need to correct 
anything?


cheers
Bruce

On Wed, 21 Jun 2017, Budge, 
Mariana wrote:




Hi Freesurfer experts,

 

I am running FS on a patient with a chronic right occipital lobe infarct as
part of a larger study. The program does not recognize the area around the
lesion as brain matter, and I am wondering how best to treat this situation.
I am worried that adding Control Points will incorrectly label the region as
white matter. I am attaching some pictures of slices where this is apparent.
Thank you so much for your help!


Best,

Mariana  


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[Freesurfer] Segmentation problem recon-all

[Lisa Delalande]

Hi,



I am a PhD student and faced a problem with Freesurfer, more specially with
segmentation. First of all, I did a typical qsub command. However, when I
cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are
often considered as grey matter.

I tried these different commands :


1.) setenv SUBJECTS_DIR /path/to/your/data

setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50'

recon-all -multistrip -clean-bm -s  -no-isrunning


2.) recon-all -skullstrip -clean-bm -gcut -subjid 

cd $SUBJECTS_DIR/yoursubj/mri/transforms

cp talairach_with_skull.lta bak

cp talairach_with_skull_2.lta talairach_with_skull.lta

recon-all -s yoursubj -skullstrip -clean-bm -clean-lta"



without success I finally used a manual method :



3.) tkmedit skullstrip3_before brainmask.mgz -aux T1.mgz



but the latter is source of error and time-consuming. I've got 105 MRI
scans to rectify. Do you have a council to improve le first step of the
reconn-all ?


Sincerely
Marine Moyon
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Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

[Elijah Mak]

Thanks Doug! It works!

Best Wishes,
Elijah 
On 21 June 2017 at 16:09:29, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

use this script  

https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table  



On 06/21/2017 10:53 AM, Elijah Mak wrote:  
> Hi Freesurfer Team  
>  
> Apologies for bumping this thread up again. I am wondering if is there  
> is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc  
> (using a similar approach such as asegstats2table)?  
>  
> Thanks for your help!  
>  
> Best Wishes,  
> Elijah  
>  
>  
>  
> On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk  
> ) wrote:  
>  
>> Hi Unix experts,  
>>  
>> I am trying to extract the PVC-ed values from gtm.stats.dat for every  
>> subject. Is there a fast way to do this using a similar workflow with  
>> asegstats2table? Thanks.  
>>  
>> Best Wishes,  
>> Elijah  
>  
>  
> ___  
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> 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  
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/  

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[Freesurfer] TRACULA -prep ERROR

[Maria Economou]

Dear Freesurfer community,

I'm having trouble completing the pre-processing step for TRACULA analysis.
I'm using a single NifTi file which I've converted using the original
DICOMS, acquired by a PHILIPS scanner. However, I get the following errors
in the command line:


dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap
ERROR: input file must be in NIfTI format
Darwin dyn143100.shef.ac.uk 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23
18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Wed Jun 21 16:22:34 BST 2017


I double-checked my configuration file and everything (bvals and bvecs)
looks like is formatted appropriately. I also tried running the command
with -i and -s flags, but i get the same errors.
Please find attached below the trac-all.log

I would really appreciate any advice as to why it's not working and what I
might be doing wrong!

Many thanks,
Maria.


trac-all.log
Description: Binary data
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Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

[Douglas N Greve]

use this script

https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table



On 06/21/2017 10:53 AM, Elijah Mak wrote:
> Hi Freesurfer Team
>
> Apologies for bumping this thread up again. I am wondering if is there 
> is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc 
> (using a similar approach such as asegstats2table)?
>
> Thanks for your help!
>
> Best Wishes,
> Elijah
>
>
>
> On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk 
> ) wrote:
>
>> Hi Unix experts,
>>
>> I am trying to extract the PVC-ed values from gtm.stats.dat for every 
>> subject. Is there a fast way to do this using a similar workflow with 
>> asegstats2table? Thanks.
>>
>> Best Wishes,
>> Elijah
>
>
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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] Using asegstats2table for gtm.stats.dat?

[Elijah Mak]

Hi Freesurfer Team

Apologies for bumping this thread up again. I am wondering if is there is a way 
to extract the ROI stats in gtm.stats.dat after mri_gtmpvc (using a similar 
approach such as asegstats2table)?

Thanks for your help!

Best Wishes,
Elijah



On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk) wrote:

Hi Unix experts,

I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. 
Is there a fast way to do this using a similar workflow with asegstats2table? 
Thanks.

Best Wishes,
Elijah 
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Re: [Freesurfer] Cortical thickness differences displayed on surface

[Ismail Koubiyr]

Dear Doug,

Thanks a lot for your help, it worked as expected.

Best,

Ismail

2017-06-20 16:31 GMT+02:00 Douglas Greve :

> Can you use annotval2surfoverlay.m ? it can be found in
> $FREESURFER_HOME/matlab or here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
>
> On 6/19/17 5:38 PM, Ismail Koubiyr wrote:
>
> Dear all,
>
> Would anyone have any idea how to display these p-values for each lobe on
> a surface ?
>
> Thanks a lot.
>
> Ismail
>
> 2017-06-15 15:02 GMT+02:00 Ismail Koubiyr :
>
>> Dear all,
>>
>> I have performed cortical thickness analysis with FS 5.3 and have found
>> some differences in some areas ( I have used the --lobesStrict option).
>> Now, I would like to display the p-values I have found for each lobe on a
>> surface . Would anyone have any idea how to do it  ?
>> Many thanks,
>>
>> Ismail
>>
>
>
>
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[Freesurfer] Regenerating Surface problems

[Michael Davies]

Hello, i have been trying to regenerate the surface on one of my subjects but 
keep having a problem where the terminal is saying there is a missing file 
name. Do you have any suggestions please?


Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj5/Subj5
bash-4.1$ recon-all -autorecon-pial -s Subj5
if: Missing file name.
bash-4.1$

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Re: [Freesurfer] error report - talairach.m3z not found

[Ramesh Babu]

Dear Douglas Greve and Bruce,

Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should I
increase memory of both or only graphic card?

Thanks
Ramesh

On Tue, Jun 20, 2017 at 9:02 PM, Bruce Fischl 
wrote:

> or don't run so many at the same time
>
> cheers
> Bruce
> On Tue, 20 Jun 2017, Douglas Greve
> wrote:
>
> >
> > The error was earlier:
> >
> > CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory.
> > Abort (core dumped)
> > ERROR: mri_ca_register with non-zero status 134
> >
> > looks like you need more memory in your gpu
> >
> > On 6/20/17 7:30 AM, Ramesh Babu wrote:
> >   Dear Expert,
> >
> > The recon-all -all process has stopped abruptly and error report shows
> > that "cannot find or read transforms/talairach.m3z". Please see the
> > attached file. Processing was running in 5 terminal simultaneously and
> > it has happened for two processing. Others exited without error. Could
> > please tell what should I do to continue the interrupted one.
> >
> > Thanks in advance
> > Ramesh
> >
> >
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[Freesurfer] glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters

[Damien MARIE]

Hi,

I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8 
mm, population 1, population 2 , and age as nuisance factor.

After POS MC simulation CW correction, I had two significant clusters resulting 
from this in the planum temporale and Heschl’s sulcus. The contrast being 
population 1 - population 2, my interpretation was higher R1 values in these 
two clusters in Pop 1 as compared to Pop 2.

After that I wanted to run some post-hoc tests let say, in a statistical 
software similar to SPSS, JMP, on the mean R1 values from each of these 
clusters. 

The strategy I picked was to stay in the common space, fsaverage, and apply 
mri_segstats:


#Extract mean R1 in montecarlo's significantcluster 

for i in `cat subjects`
do mri_segstats --mul 1000 --annot fsaverage lh PT_mc-z.pos.sig.ocn --i 
$SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.PT.R1.${i}.stats
done

for i in `cat subjects`
do mri_segstats --mul 1000 --annot fsaverage lh HS_mc-z.pos.sig.ocn --i 
$SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.HS.R1.${i}.stats
done



Everything when fine but as compared to my glm analysis when looking at mean 
group differences in my stat software I have the opposite  : larger R1 values 
in Pop 2 as compared to Pop 1 (after removing the effect of age or not, and 
removing one outlier or not).

I went back to my glm and checked everything, fsgd file, matrix and so on, 
everything seems ok I am not mistaken on the direction of my glm contrast (pop 
1 - pop 2) so I do not get it at all.

Any advices?

For now I am thinking about going back in the individual space, registering my 
clusters in the individual surfaces (label2surf something like that) and then 
extract my mean R1 values, or  extract values in non-smoothed maps, but I do 
not think it will change anything.


Damien



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