Shared Group Space Projections#
This guide explains how to project data from an individual subjects space into a shared group space (i.e. fs-average space). This step is necessary if the data is to be analyzed on a group scale or projected onto an atlas.
Group space projections#
The following code demonstrates how to project data into fs-average space.
finnpy.src_rec.subj_to_fsavg.prepare(fs_path, anatomy_path, subj_name)
subj_to_fsavg_mdl = finnpy.src_rec.subj_to_fsavg.compute(cort_mdl, anatomy_path, subj_name, fs_path, overwrite)
src_fsavg_data = finnpy.src_rec.subj_to_fsavg.apply(subj_to_fsavg_mdl, src_data)
(src_avg_data, morphed_channels, region_names) = finnpy.src_rec.avg_src_reg.run(src_fsavg_data, subj_to_fsavg_mdl, fs_path)
fs_path points towards the FreeSurfer installation. The FreeSurfer folder should contain the ‘bin’ folder, license.txt, and sources.sh (among other files/directories).
anatomy_path contains sub-folders with anatomy folders for all subjects. FreeSurfer will fail if a subjects folder already exists.
subj_name is the name of the subject.
overwrite Boolean flag whether to overwrite MRI maps. Defaults to False.
src_data Source space data. Currently in the source space of the respective subject.
subj_to_fsavg_mdl Preliminary result.
src_fsavg_data Data projected into fs-average space.
src_avg_data Data segmented according to the Desikan-Killiany atlas.
morphed_channels List matching fs-average channels with atlas regions.
region_names Names of the respective Desikan-Killiany atlas regions.
Projection into atlas space#
After projecting the data from their individual subject’s space into fs-average space for group analyses, the Desikan-Killiany atlas may be employed to cluster regions, significantly decreasing channel count and also variability across subjects.
(src_avg_data, morphed_channels, region_names) = finnpy.src_rec.avg_src_reg.run(src_fsavg_data, subj_to_fsavg_mdl, fs_path)