It looks like in the tutorial, mri_glmfit is invoked from the directory where
‘—y’ input file is located. Try to prepend the directory of your processed data
to ‘—y’ input.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Maria Czarnecka
Sent: Sunday, March 2, 2025 7:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] cortical thickness group analysis
External Email - Use Caution
Hello,
I am trying to run a group analysis on cortical thickness (two groups, no
covariates). I have been trying to follow the tutorial
(FsTutorialGroupAnalysis) but I run into a problem with the mri_glmfit. My
script looks like this:
fspath="/dat/freesurfer"
for hemi in lh rh; do
echo $hemi
cd $fspath
mri_glmfit \
--y ${hemi}.norm_${hemi}_thickness.mgh \
--fsgd /dat2/maria/scripts/final/group.fsgd dods \
--C /dat2/maria/scripts/final/group.diff.mtx \
--surf fsaverage ${hemi} \
--cortex \
--glmdir ${hemi}.group.diff.glmdir
done
I think the function is searching for " --y ${hemi}.norm_${hemi}_thickness.mgh"
in the main freesurfer directory instead of going into each participant's
folder. What am I missing? The first error that i get is:
" ...
FSGD /dat2/maria/scripts/final/group.fsgd
labelmask /dat/freesurfer/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.group.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.group.diff.glmdir
Loading y from /dat/freesurfer/lh.norm_lh_thickness.mgh
error: mghRead(/dat/freesurfer/lh.norm_lh_thickness.mgh, -1): could not open
file
... done reading.
ERROR: loading y /dat/freesurfer/lh.norm_lh_thickness.mgh
..."
Does it mean that something is wrong with my group.fsgd file?
A sample of this file, just in case:
"
GroupDescriptorFile 1
Title ThickBlinds
Class Class1 plus blue
Class Class2 circle green
Input sub-NW01W Class1
Input sub-NW02W Class1
..."
I will be grateful for your help.
Best,
Maria Czarnecka
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