Working with ROIs (Freesurfer)

The .label files created during autorecon3, or by saving an overlay are plaintext lists of vertices. It should be straightforward to find the intersection or union of the vertices in two or more .label files using common Unix shell commands.

.label Syntax

Below is the first few lines of the lh.banksts.label file for a participant. This file was produced during the Lausanne parcellation procedure.

#!ascii label  , from subject FS_0043 vox2ras=TkReg
1457
32992  -47.867  -62.891  33.007 0.0000000000
32993  -48.881  -62.907  32.963 0.0000000000
34014  -47.298  -61.696  33.538 0.0000000000
34015  -47.972  -61.259  33.648 0.0000000000
34024  -47.634  -62.264  33.251 0.0000000000
34025  -48.286  -61.775  33.303 0.0000000000
...etc

The first line is a header line. The second line indicates the number of vertices in the label file. The remaining lines indicate the vertex number, x,y,z coordinates of the vertex, and I have no idea what that last column indicates but it's not terribly important for our purposes.

Preparation of .label Files

The steps described below do not work on .annot files because they are not plaintext and easily manipulated. However, mri_annotation2label will convert a .annot file to a series of .label files.

e.g. mri_annotation2label --annotation cache.th13.abs.sig.ocn --hemi rh --subject fsaverage --surf pial --labelbase rh.T1

Set Operations on .label Files

Intersecting .label Files (Intersection)

Given what we know about the contents of a label file, the unix comm command should suffice to find the common entries between two label files, which is the set intersection of vertices appearing in each.

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011743.html

Merging .label Files (Union)

A union operation will find all vertices appearing in either .label file. You will want to make sure that only unique values are retained (i.e., you don't want to list the same vertex multiple times in the output .label file).