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
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 tutorialhttps://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: agoneill@mgh.harvard.edumailto: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
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-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 <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: agoneill@mgh.harvard.edu <mailto: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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
O'Neill, Alexandra Grace