oops, sorry, that should have been sphere not sphere.reg On 09/25/2014 01:35 PM, Reza Rajimehr wrote: > 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 > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
