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In order to compute the contrats you will first need to change to the tutorial data directory and setup SUBJECTS_DIR: In order to compute the contrasts you will first need to change to the tutorial data directory and setup SUBJECTS_DIR:
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[wiki:FsTutorial top] | [wiki:FsTutorial/GroupAnalysis previous]

  • To follow this exercise exactly be sure you've downloaded the [wiki:FsTutorial/Data tutorial data set] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.

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.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.

FsTutorial/ComputeContrast (last edited 2021-09-22 11:38:51 by DevaniCordero)