cd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
/Applications/freesurfer/bin/mri_glmfit-sim
--debug --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --sim mc-z 5000 1.302 lh_mc-z.abs_5000p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25

FreeSurferEnv.csh 7.1.1
Mon Jun 28 07:34:24 CEST 2021
Darwin upddkp224.unibe.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu May  6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
jurgenhanggi
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex

DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.595954
nSimPerJob = 5000
1/1 Mon Jun 28 07:34:24 CEST 2021
mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug
simbase IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001
FWHM = 14.595954
gdfRead(): reading IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd

WARNING: carriage returns have been detected in file IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd
Was it created on a Windows computer?
This may cause an error in reading the FSGD file.
If so, try running:
    cat IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd | sed 's/\r/\n/g' > new.IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd 
Then use new.IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd 

INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65417.000000
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195472
Surface smoothing by fwhm=14.595954, niters=157.000000

7.1.1
cwd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
cmdline mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug 
sysname  Darwin
hostname upddkp224.unibe.ch
machine  x86_64
user     jurgenhanggi
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
fwhm     14.595954
niters    157.000000
OneSampleGroupMean 0
y    /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
logyflag 0
usedti  0
FSGD IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd
mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
   ... done reading.
ERROR: loading y /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force