Thanks! Now it is working!
Final questions...I hope:
- Does the vertex order remain the same in all the successive files? If the vertices are in the order V1,....., VN in lh.orig, will I find them in the same order in lh.sphere, and then in lh.sphere.reg?
- I am trying to use tksurfer to visualize the different surfaces. I am running on a Mac (Mac OS X, Lion, 10.7.5), and I have XQuartz 2.7 installed. When I execute for example: tksurver bert lh inflated (as described on the wiki), the program starts X11, seems to be reading all files correctly, but them it prints: surfer: tkoInitWindow(bert) and...nothing happens. X11 indicates that there is a window "Bert", but does not display it.
Note that freeview is working, so it is not essential that I get tksurfer running.
Thanks again for your great help!
-Patrice
On Thu, 13 Dec 2012, Bruce Fischl wrote:
I knew I would forget something :)
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
Bruce
On Thu, 13 Dec 2012, Patrice Koehl wrote:
Hi Bruce,
Thanks for your prompt answer!
I have started working on your suggestions...it has worked so far, but I am reaching a small problem. Let us say I have two subjects, Subject1 and Subject2. For each, I was able to generate lh.orig, and subsequently lh.smoothwm (and lh.aread, lh.curv), then lh.inflated (and lh.sulc), and finally lh.sphere. However, when I try to register, using for example: mris_register -1 lh.sphere ../Subject1/lh.sphere ./lh.sphere.reg I get the error message: could not read curvature file '../Subject1/lh.inflated.H'
How do I generate this missing file?
Thanks in advance,
-Patrice
On Thu, 13 Dec 2012, Bruce Fischl wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.