Anatomy Pipeline

We collect a high resolution T1-weighted image on every subject, and use this image to define the coordinate space for all subsequent analyses. This section describes the processing steps for a subject's T1-weighted anatomy and should be performed before analyzing the rest of their MRI data.

AC-PC Aligned Nifti Image

Data can come off the scanner with arbitrary header information and in parrec format. So for each subject we start by defining a coordinate frame where 0,0,0 is at the anterior commissure, the anterior and posterior commissure are in the same X and Z planes, and the mid-line is centered in the image. Bob Dougherty wrote a nice tool to help with this. See mrAnatAverageAcpcNifti. The subject's T1-weighted image should be ac-pc aligned, resliced (preserving its resolution), and saved in the subject's anatomy directory.

cd /home/projects/MRI/[subid]
parrec2nii -c --scaling=fp *.PAR
im = niftiRead('T1path')
mrAnatAverageAcpcNifti({'T1path'}, '/home/projects/anatomy/[subid]/t1_acpc.nii.gz', diag(im.qto_xyz))