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FreeSurfer GLM Tutorial
cd /blue/clp7934/share/Module5 #Go into the Module 5 directory
cp tutorial_data.tar.gz ../{your gatorlink}/ #Copy tutorial_data.tar.gz from Module5 into your personal directory
cd ../{your gatorlink} #Go into your directory
tar -xzvf tutorial_data.tar.gz && rm tutorial_data.tar.gz #extract the tutorial data and then remove the .tar.gz file. This will take a while to complete
cd tutorial_data_20190918_1558 #Go into the tutorial data directory
rm -fr dicom_challenge/ diffusion_recons/ diffusion_tutorial/ fsfast-functional/ fsfast-tutorial.subjects/ practice_with_data/ #Remove some unnecessary data
cd tutorial_data_20190918_1558/buckner_data/tutorial_subjs/group_analysis_tutorial #change into the group analysis tutorial directory
module load freesurfer #Make FreeSurfer available to use
export SUBJECTS_DIR=$PWD #set FreeSurfer's subjects directory to your current location. Alternatively, you can put in the whole path after the equal sign
echo $SUBJECTS_DIR #This will verify that SUBJECTS_DIR really is your current location. Make sure the path printed to the screen is where you think you are.
cd glm && ls #go in the GLM directory and display contents. The && runs the ls command if the previous command successfully completed.
You do not need to run what's in the next block of code
mris_preproc --fsgd gender_age.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.gender_age.thickness.00.mgh
mri_surf2surf --hemi lh \
--s fsaverage \
--sval lh.gender_age.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.gender_age.thickness.10.mgh
This is the end of the code that has already been run. Run everything after this.
This next command runs the general linear model, which is a linear regression. What you are testing is if there is a relationship between cortical thickness and age, adjusting for sex
mri_glmfit \
--y lh.gender_age.thickness.10.mgh \
--fsgd gender_age.fsgd dods \
--C lh-Avg-thickness-age-Cor.mtx \
--surf fsaverage lh \
--cortex \
--glmdir lh.gender_age.glmdir
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=1,5 -viewport 3d -layout 1