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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 C.] 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 can do the smoothing step:
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 can move on to test your contrast vector:
mri_glmfit --y lh.my_gender_age.thickness.10.mgh --fsgd my_gender_age.txt --glmdir lh.my_gender_age.glmdir --pca --surf --average lh --C age.mat
The commands are the same for the right hemisphere, replacing every lh with an rh.