Hi Rouhi

it's hard to tell from looking at the sphere.reg by itself. In general though if the parcellations are correct then the registration must be pretty good.

cheers Bruce On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:

Dear Bruce I checked the parcellation and look quiet OK. I attached two subjects , whcih subj_1 shows bad registration to fsaverage  and subj_2 shows the good registration.  I attached a file which compare two subjects according to sphere and sphere.reg. For the subj_1 , it has more figures to see how the parcellation is.  Thanks in advance

Best Rouhi

On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rouhi

  check the parcellations. If they are correct then the sphere.reg must be pretty accurate.

  cheers
  Bruce

On Thu, 11 Aug 2011, Rouhollah Abdollahi 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