This page describes the workflow necessary to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in volume space.

For this workflow, assume the following data is present:

1) an ROI mask in the form of a volume file, where the voxel value is '1' in the ROI, and '0' elsewhere. the coordinate space of that volume is irrelevant.

2) an anatomical (T1) volume file of the subject used to create the ROI mask volume, in the same coordinate space as the ROI mask.

2) processed freesurfer data for a subject (or set of subjects), that is, recon-all -s <subj> -all has run to completion, producing subject surfaces and cortical thickness data.

The general workflow consists of these steps:

1) create a registration from the ROI-anatomical volume to a freesurfer template subject, preferably the 'fsaverage' subject (which is the recommended template subject). to perform this registration, use either an automatic method, such as fslregister or spmregister, or a manual method, via tkregister. fslregister and spmregister utilities are freesurfer wrappers for fsl's flirt and spm's spm_coreg. for example, if the name of the ROI mask volume is abc.nii, then this command:

  spmregister --s fsaverage --mov /path/to/abc.nii --reg abcroi_to_fssaverage.dat

type fslregister --help}} or {{{spmregister --help for details.