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 ...)
- Create a template from a single subject
make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg
- Register each subject to this template, including first
subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster.
foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end
- Create a new template from all subjects using the new registration
make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg
- Register each subject to this new template
foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end
- 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:
- 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.
- Make a template from "S1 and S2" through the procedure described at
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingare.... 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
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