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 inthis 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>
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