I've included hooks into make_average_subject and recon-all to make this much easier. make_average_subject will create the template (.tif) files from the subjects you specify, then you just run recon-all with -surfreg-to-subject averagesubjectname.
Bruce Fischl wrote:
On Wed, 16 Jan 2008, Graham Wideman wrote:
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:
- 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.)
I think it recomputed the curvature internally instead of reading the file.
- 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?
it needs to read the subject's ?h.sphere.reg, but the gcs is already in register with the atlas, so it doesn't need one for the .gcs (which is actually a bunch of info stored in different level icosahedral meshes)
- 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.)
mris_make_template creates an "average" sphere.reg (actually a bunch of means and variances of different geometric features. To make a new gcs file use mris_ca_train.
- What, if any, is the relationship between
.../freesurfer/average and .../freesurfer/subjects/fsaverage
average is a catch-all for various "average" files, like volume statistics, tal atlases, etc..., fsaverage is the subject made from averaging our 40 manually labeled subjects
cheers, Bruce
Thanks,
Graham _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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