Hi Rouhi
I don't really understand. Are you saying you transformed the initial image before giving it to recon-all? There is a switch to mris_register to initialize with the tal xform, but we never use it as in pretty extensive tests it didn't seem to help. mris_register has a very large initial capture range due to it's global search, so I would be surprised if the initial orientation was the problem.
cheers Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
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.com wrote: 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.edu wrote: 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
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.
-- With Best Regards Rouhollah Abdollahi
-- With Best Regards Rouhollah Abdollahi