Reading FreeSurfer morphometry data in R

read_freesurfer_morph.R

#!/usr/bin/env Rscript
#
# This script illustrates how to load FreeSurfer morphometry data in R.
#
# If you do not have 'freesurferformats' yet, you need to install it:
# install.packages('freesurferformats');

library('freesurferformats');

subjects_dir = "~/data/study1";  # Replace with your data (or with example data from the 'fsbrain' package).
subject = 'subject1';


# Example for native space data: read the file $HOME/data/study1/subject1/surf/lh.thickness
thickness_native_lh = freesurferformats::read.fs.morph(file.path(subjects_dir, subject, 'surf', 'lh.thickness'));


# Example for standard space data
thickness_std_fwhm10_lh = freesurferformats::read.fs.morph(file.path(subjects_dir, subject, 'surf', 'lh.thickness.fwhm10.fsaverage.mgh'));

# Optional: you should now have a look at your data. E.g., you could try:
hist(thickness_native_lh);
hist(thickness_std_fwhm10_lh);