Hi Patrice
you can use mris_register with the -1 switch to indicate that the target is a single surface not a statistical atlas. You will however still have to create the various surface representations and geometric measures we expect (e.g. ?h.inflated, ?h.sulc, etc....). If you can convert your surfaces to our binary format (e.g. using mris_convert) to create an lh.orig, it would be something like:
mris_smooth lh.orig lh.smoothwm mris_inflate lh.smoothwm lh.inflated mris_sphere lh.inflated lh.sphere mris_register -1 lh.sphere $TARGET_SUBJECT_DIR/lh.sphere ./lh.sphere.reg
I've probably left something out, but that basic approach should work.
cheers Bruce
On Wed, 12 Dec 2012, Patrice Koehl wrote:
Dear FreeSurfer experts,
I apologize in advance if my questions seem naive or too simple: I am completely new to FreeSurfer and I am still attempting to understand how to make good use of its potential.
I believe I want to use it in an unusual way. I have been given two cortical surfaces, both in the form of genus 0 triangular meshes. The two meshes are stored as OFF files, but I can easily generate other formats (PLY, OBJ, simple ASCII, ...). For both surfaces I also have informations on some sulci, in the form of list of vertices, in ASCII format.
I would like to map (register) one mesh onto the other: it seems that FreeSurfer would allow me to do this with the following steps:
- inflate the two surfaces
- map them onto the sphere
- register one surface (on the sphere) onto the second surface (on the
sphere).
How do I make this work? I have looked at "SurfaceRegAndTemplates", but the process described relates to specific FreeSurfer files. I will obviously need to convert my OFF files into a format that FreeSurfer can recognize, and vice versa convert the sphere representations (Source mesh, S, target mesh, T, and S on T) into an ascii format that I can analyze. Could someone give me an overview of how I should proceed, with pointers on which procedures I should use from FreeSurfer.
Thanking you in advance for your help,
Best regards,
-Patrice
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