Can you send the log file for the 2nd mris_preproc command?
On 2/8/2021 4:52 PM, Larissa Bechtle wrote:
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Hi everybody, I ran the following commands which worked out fine for my Group Analysis. Just like in the wiki-Tutorial available I focused on the thickness of my probands brains at first.
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt
recon-all -s ab35 –qcache
mris_preproc --fsgd FSGD.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gewalt.10.mgh
mri_glmfit --y lh.gewalt.10.mgh --fsgd FSGD.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir leftuncorrected.glmdir
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=leftuncorrected.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5-viewport 3d
Currently I am tryig to run the same Group Analysis but now focusing on the volume instead. Thus I tried to change my commands. I ended up with the same image as in my previous Group Analysis (which focused on hickness instead of volume) and I dont really get why. I would be very grateful for any support. Best wishes Larissa
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt
mris_preproc --fsgd FSGD.fsgd --cache-in volume.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gewalt_volume.10.mgh
mri_glmfit --y lh.gewalt_volume.10.mgh --fsgd FSGD.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lefttuncorrected_volume.glmdir
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=leftuncorrected_volume.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5-viewport 3d
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