This document describes how to perform a paired analysis in FreeSurfer. This includes a two time-point longitudinal analysis in which the same subject was scanned twice with each scan being run through FreeSurfer separately (using the longitudinal stream). It also includes a cross-over analysis in which each subject of a cohort has a matching subject in another cohort. In either, case this describes how to perform statistical tests on the difference between the pairs.

Overall Strategy

  1. Sample each individual's surface onto the average surface.
  2. Compute the difference between each of the pairs in the average surface space.
  3. Concatenate the differences into one file.
  4. Smooth on the surface (optional)
  5. Perform analysis with mri_glmfit on this file

Steps 1-3 will be performed by one command (mris_preproc), step 4 by mri_surf2surf, and step 5 by mri_glmfit. Two FSGD files will be required, one for Steps 1-3, and one for Step 5.

Create the First [[FsgdFormat|FSGD]] File

The first FSGD file just needs the subject names of the inputs. The matching pairs must be listed consecutively. You do not need to specify groups or variables at this point (that is needed below) -- you can, it is just not needed. Eg, if you created the file below and called it "pairs.fsgd" 

GroupDescriptorFile 1
Class Main
Input subject1      Main
Input subject1match Main
Input subject2      Main
Input subject2match Main
Input subject3      Main
Input subject3match Main
Input subject3      Main
Input subject3match Main

where subject1match is the match for subject1 (either another time point or a match based on some sort of demographic).

Run mris_preproc

The mris_preproc command will be: 

  mris_preproc --target fsaverage --hemi lh \
   --meas thickness --out lh.paired-diff.thickness.mgh \
   --fsgd pairs.fsgd --paired-diff

This peforms Steps 1-3 above, saving the data to lh.paired-diff.thickness.mgh. The key difference between this invokation and a "norma" invocation is the addition of the --paired-diff argument. This tells mris_preproc to compute the difference between the first and second, the third and fourth, etc. This has two implications: