How to load FreeSurfer morphometry data in R, transform it and save as new file

read_write_freesurfer_morph.R

#!/usr/bin/env Rscript
#
# This script illustrates how to load morphometry data in R, apply some
# transformation (a simple log in this example), and save the result
# to a new file.
#
# If you do not have 'freesurferformats' yet, you need to install it:
# install.packages('freesurferformats');

library('freesurferformats');

subjects_dir = "~/data/study1";
subjects_list = c("subject1", "subject2");
measure = 'thickness';

# Example for native space data
for (sj in subjects_list) {
    for (hemi in c('lh', 'rh')) {
        morph = freesurferformats::read.fs.morph(file.path(subjects_dir, sj, 'surf', sprintf('%s.%s', hemi, measure)));
        freesurferformats::write.fs.morph(file.path(subjects_dir, sj, 'surf', sprintf('%s.%s_log', hemi, measure)), log(morph));
    }
}



# Example for standard space data
template_subject = 'fsaverage';
fwhm = '10';

for (sj in subjects_list) {
    for (hemi in c('lh', 'rh')) {
        morph = freesurferformats::read.fs.morph(file.path(subjects_dir, sj, 'surf', sprintf('%s.%s.fwhm%s.%s.mgh', hemi, measure, fwhm, template_subject)));
        freesurferformats::write.fs.morph(file.path(subjects_dir, sj, 'surf', sprintf('%s.%s_log.fwhm%s.%s.mgh', hemi, measure, fwhm, template_subject)), log(morph));
    }
}