Doug and Bruce:
Bruce says:
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.
Side point -- the "bunch of means and variances"... that sounds more like the template or GCS file than the average sphere.reg, which I thought was a mesh, right?)
Doug says:
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.
Are these two suggestions alternates or complementary in some way? A major gap for me is this:
Supposing we start with 10 subjects, to be used in creating a new average sphere, tif and gcs for labels, later to be used for many more subjects. These initial 10 subjects are processed by freesurfer, and hence have all their surfaces, (along with ?h.sphere.reg and annot files, courtesy of the default average sphere, tif and label gcs --- which we don't want to use ultimately.)
What then are the steps to create a *new* average sphere and tif?
My assumption has been that some program reads the 10 individuals' ?h.sphere (not reg) files, plus their curv and sulc files, and by clever average, warp and whatever on spherical surface, it produces an average ?h.sphere along with corresponding average curv and sulc tif file. I'm expecting these to be done in one step, because without a curv/sulc tif file the new average sphere is meaningless I think.
I'm specifically *not* expecting that the process involves averaging the individual white surfaces (possibly including talairaching), followed by inflating the average white surface to a sphere. And because I have the impression that this is the kind of thing that make_average_surfaces (called by make_average_subject) does, I'm resistant to thinking that make_average_subject is part of the answer here.
So... I'm all ready to think that mris_make_template is the program to do the job... but I don't see anywhere in the source code where it writes out a surface.
(FWIW I do see that mris_ca_train is used to create the GCS file -- I don't have any questions on that part.)
And finally: Bruce wrote:
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
...so I'm getting the impression that some of the {fshome}/average files are not related to the fsaverage subjects (such as mni 305 files), and some perhaps are (like lh.average.curvature.filled.buckner40.tif)... and some others... not sure.
On this point, mainly I'm trying to understand what common sphere and tif file are used in a normal recon-all run, and where they came from (and trying to follow recon-all call's args into mris_register is puzzling).
Thanks,
Graham