segmentation_centers: Find center of mass of regions in a brain volume...

In dfsp-spirit/brainloc: Find Region Names and Coordinates for a Point on the Human Brain

Description

Find center of mass of regions in a brain volume segmentation.

Usage

segmentation_centers(volatlas, named_regions = NULL, vox2ras = diag(4))

Arguments

volatlas	3d integer array, the brain volume segmentation. Can be an fs.volume instance. Typically something like 'subject/mri/aseg.mgz'.
named_regions	the regions to consider, a named list where the keys are character strings: the region names from the colorLUT, and the values are integers: the region codes from the volume. See name_regions to get one. Can be NULL, in which case all regions in the volatlas will be used, and the region names will appear as 'region_x', where 'x' is the integer region code in the volatlas.
vox2ras	4x4 numerical matrix, the voxel to RAS coordinate transformation matrix for the volume. If NULL and volatlas is an fs.volume instance, the function will try to extract it from the volume header. The default is the identity matrix, which will return voxel indices instead of RAS coordinates.

Value

data.frame with region names and the center of mass x, y and z coordinates for the regions.

Examples

## Not run: 
if(has_fs()) {
fsh = fs_home();
lutfile = file.path(fsh, "FreeSurferColorLUT.txt");
segfile = file.path(fsh, 'subjects', 'fsaverage', 'mri', 'aseg.mgz');
named_regions = name_regions(segfile, lutfile);
named_regions$Unknown = NULL; # Ignore an atlas region.
sc = segmentation_centers(segfile, named_regions);
regions_distance_matrix = dist(sc);
}

## End(Not run)

dfsp-spirit/brainloc documentation built on Jan. 28, 2022, 12:25 p.m.