I’m looking for advise on how to prepare the Desikan-Killiany atlas for inclusion in qsiprep.
This entails transforming the fsaverage aparc+aseg segmentation into MNI152NLin2009cAsym space (LPS+ without sform).
What I tried was:
Run mri_label2vol using the MNI152NLin2009cAsym atlas like so:
mri_label2vol --temp mni_1mm_t1w_lps.nii.gz --seg aparc+aseg.mgz --reg $FREESURFER_HOME/average/mni152.register.dat --o aparc_aseg_mni152.nii.gz
Since mni152.register.dat is based on a MNI152 template in LAS format, I manually flipped the data along the Y dimension using Matlab functions.
While the result looked resonable, this dis not take care of the sform issue. I tried reading the header from one of the atlases included with qsiprep with niftiinfo in Matlab and write back the data to disk using that, which did not lead to a valid brain image, so whatever format is used in qsiprep does not seem compatible with the Matlab functions.
I also have my doubts about using mni152.register.dat since I beleive this is based on an earlier MNI template version.
I have a feeling the solution is much cleaner/simpler than what I am doing. Any hints/tips/suggestions are welcome!