mmm, still not sure. I'm assuming that you don't really have those
backslashes ("\") in there. Can you try it with mcz instead of perm just
to see if you can get it running. I would also try version 7.4.1;
version 6.0 is from a long time ago and so hard to debug.
On 1/19/2024 3:03 PM, O'Neill, Alexandra Grace wrote:
Hi Doug,
Thanks so much for getting back to me. Below is our previous
correspondence:
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm>
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: agone...@mgh.harvard.edu
<mailto:agone...@mgh.harvard.edu>
Thank you,
Alexandra
------------------------------------------------------------------------
*From:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
*Sent:* Friday, January 19, 2024 2:44 PM
*To:* O'Neill, Alexandra Grace <agone...@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
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