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Group Analysis command lines
In order to compute the contrats you will first need to change to the tutorial data directory and setup SUBJECTS_DIR:
cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial setenv SUBJECTS_DIR ${PWD}
Change into the directory you ran the estimation step in, most likely called 'stats':
cd stats
Upon successful completion of the make_average_subject command you should have an average subject in your SUBJECTS_DIR. After successfully completing [wiki:FsTutorial/CreateFsgdFile Exercise A.] and [wiki:FsTutorial/CreateContrastVectors Exercise B.] you should have an FSGD file called my_gender_age.txt and a contrast file called age.mat, both in your SUBJECTS_DIR/stats directory . The following are sample commands, that can be used with the data, to complete a group analysis:
# For the left hemisphere mris_preproc --fsgd my_gender_age.txt --target average --hemi lh -- meas thickness --out lh.my_gender_age.thickness.mgh
Once this completes you should see the file lh.my_gender_age.thickness.mgh. The next step, the smoothing step, will use this as input:
mri_surf2surf --hemi lh --s average --sval lh.my_gender_age.thickness.mgh --fwhm 10 --tval lh.my_gender_age.thickness.10.mgh
Once this is complete you should see the file lh.my_gender_age.thickness.10.mgh. The next step will test the hypothesis you've set up using your contrast vector:
mri_glmfit --y lh.my_gender_age.thickness.10.mgh --fsgd my_gender_age.txt doss --glmdir lh.my_gender_age.glmdir --pca --surf --average lh --C age.mat
You should have two new directories in FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial/stats - lh.my_gender_age.glmdir and rh.my_gender_age.glmdir. If you do:
ls lh.my_gender_age.glmdir
you should see this:
age/ beta.mgh fsgd.X.mat pca-eres/ rvar.mgh y.fsgd ar1.mgh eres.mgh mri_glmfit.log rstd.mgh Xg.dat
and if you do:
ls lh.my_gender_age.glmdir/age
you should see this:
C.dat F.mgh gamma.mgh maxvox.dat sig.mgh
You can view your results by opening the average subject in tksurfer:
tksurfer average lh inflated
and loading in your overlay, File -> Load Overlay and browse to stats/lh.my_gender_age.glmdir/age/sig.mgh. If you would like to also view the scatter plots associated with this you can do so by File -> Load Group Descriptor File and browse to stats/lh.my_gender_age.glmdir/y.fsgd.
The commands are the same for the right hemisphere, replacing every lh with an rh.