Dear Bruce

I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around  X axis?  and apply this rotation to all data set?

Best
Rouhi


On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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


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--
With Best Regards
           Rouhollah Abdollahi






--
With Best Regards
           Rouhollah Abdollahi







--
With Best Regards
           Rouhollah Abdollahi