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

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