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Group Analysis command lines

In order to compute the contrasts 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_fsgd.txt and a contrast file called age.mat, both in your SUBJECTS_DIR/stats directory. Confirm that those files exist:

ls my_gender_age_fsgd.txt age.mat

If my_gender_age_fsgd.txt does not exist, complete [wiki:FsTutorial/CreateFsgdFile Exercise A.] If age.mat does not exist, complete [wiki:FsTutorial/CreateContrastVectors Exercise B.]

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_fsgd.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.