Hi Doug,

Thanks so much for getting back to me. Below is our previous correspondence:

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Date: Friday, January 12, 2024 at 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issue with mri_glmfit-sim

I think v6 might be broken when using -bg. Try removing that.

On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote:

Hello FS community,

 

To correct for multiple comparisons for the results of a parametric modulation GLM analysis, I have run mri_glmfit-sim using Freesurfer version 6.0 with the following command:

 

mri_glmfit-sim \ --debug --glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm \ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1

 

The code completes without errors, however none of the output files mentioned in this tutorial are created. Below are the contents of the mriglm-fit.log file in case that is helpful.



$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ 

cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago

cmdline mri_glmfit.bin --y /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz --wls /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz --fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm --glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM --surf fsaverage rh --fwhm 6 

sysname  Linux

hostname tempest.nmr.mgh.harvard.edu

machine  x86_64

user     ago5

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

fwhm     6.000000

niters    26.000000

OneSampleGroupMean 1

y    /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz

logyflag 0

usedti  0

FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd

labelmask  /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label

maskinv 0

glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM

IllCondOK 0

ReScaleX 1

DoFFx 0

wFile /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz

weightinv  1

weightsqrt 1

ResidualFWHM 12.847434

SearchSpace 74490.844410

anattype surface

 

 

 

Do you have any idea how to fix this problem? Thanks so much in advance!

Alexandra



Alexandra G. O'Neill (she/her)

Clinical Research Coordinator
Massachusetts General Hospital
Department of Psychiatry
Division of Neuropsychiatry and Neuromodulation
149 13th Street, Charlestown, MA 02129

T: (617) 726-8753 | E: agoneill@mgh.harvard.edu


Thank you,
Alexandra
From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Friday, January 19, 2024 2:44 PM
To: O'Neill, Alexandra Grace <AGONEILL@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issue with mri_glmfit-sim
 
Sorry, I already forgot  what the problem was. Can you include our previous correspondence? Also, make sure to reply to the list. Thanks!

On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:

Hi Doug,

 

Thank you for getting back to me. Unfortunately, the issue is persisting, and the command is still running but with no output files. Is there anything else that could potentially be the problem? I’m attaching the most recent log file (as a txt file) from the command I ran. Please let me know if any other information would be helpful!

 

Thank you so much,

Alexandra