Thank you Doug for your comprehensive response. This looks clear, and I am going to try it out. Just one question for now:
In step 1 (create a template from a single subject), I do not yet have "sphere.reg". Should I write "--surf-reg sphere"? make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere Reza Hi Reza, I think that this should work. doug set subjectlist = (subject1 subject2 ...) 1. Create a template from a single subject make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg 2. Register each subject to this template, including first subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster. foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end 3. Create a new template from all subjects using the new registration make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg 4. Register each subject to this new template foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end 5. Return to step 3. Iterate 4 or 5 times to remove the dependence on the first subject. When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX On 09/19/2014 10:24 AM, Reza Rajimehr wrote: > Hi, > > I have a question about spherical registration, and I couldn't find a > relevant answer in the mailing list. > > I have two subjects S1 and S2 with corresponding functionals. I want to > show the functionals of each subject on the surfaces of the third subject > S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg > files yet because these are monkey subjects and I did not want to register > them to the buckner40.tif template. Since my goal is not group averaging, > and it is just to map functionals to the same-subject anatomicals and then > to the target-subject anatomicals, I was thinking of one of the following > solutions: > > 1) Convert sphere of S3 to a template .tif file, then use mris_register to > register spheres of S1, S2, and S3 to that template and generate > sphere.reg for all the subjects. Not sure if mris_make_template works for > one subject though. > > 2) Make a template from "S1 and S2" through the procedure described at > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingaregistrationtemplatefromscratch.28GW.29. > Then register S1, S2, and S3 to that template and generate sphere.reg for > all the subjects. > > Which approach is recommended? > > BTW, I do not know of a monkey template that is based on the surfaces from > a large group of monkeys. > > Thanks for any advice, > Reza _______________________________________________ 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.
