Folks:
I'm trying to get a complete picture of what's entailed in creating our own atlas, including our own average reference sphere, so if there's a doc on this specific subject I'd love to see it.
Absent that, below are questions to fill in some gaps:
1. Normal spherical reg: mris_register's command-line params don't include all files it must read, so I'm looking for a list of all the files that it reads under the usual circumstances (ie: registration to ref sphere; registration to opposite hemi), and how it decides *which* files to read. (Amongst other discrepancies, when recon-all runs, mris_register doesn't seem to read ?h.curv, whereas various postings suggest that it does.)
2. Normal labeling with mris_ca_label: Presumably this only works if subjects are registered to the same average sphere mesh as was used to create the chosen GCS file, right? Yet mris_ca_label doesn't need to read that actual ?h.sphere.reg file because equivalent position-on-sphere info is contained in the GCS file... right?
3. Creating one's own average reference sphere: What progam(s) does one use to create the average ?h.sphere(.reg?) file (presumably from each subject's ?h.sphere file)? and average curvature file (ie: the tif file)? FWIW, it looks like mris_make_template is somehow involved here, but it's entire documentation consists of just "This program will add a template into an average surface" (what does that mean?), and the source code looks like it only produces the tif file containing average sulc and curv data. (From which I conclude the here, "template" refers to just that file.)
4. What, if any, is the relationship between .../freesurfer/average and .../freesurfer/subjects/fsaverage
Thanks,
Graham