Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem.
Thanks for your quick response.
On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi roohy466@gmail.comwrote:
Dear Bruce
I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create caret surfaces. when I look at my subjects' surfaces I can see in flat map in caret some of subjects sulci patterns are really distorted and I think it is related to sphere registration to fsaverage sphere. Beacsue the code is using sphere.reg to create all surfaces. for the subjects which I have less distortion on sulci pattern I have good data (3 subjects) but for the (9 subjects) rest it seems they have problem to register to fsaverage. Is there any way that I can be sure that sphere.reg properly created?
Thank you very much
Rouhi
On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Try using fsaverage as the trgsubject Cheers Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi roohy466@gmail.com wrote:
.V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg
sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear freesurfer experts
I've tried to export my label file from individual space to fsaverage
space by using this command:
mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject
SUB1 --trglabel rh.V1_reg.
like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage
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-- With Best Regards Rouhollah Abdollahi