Dear Bruce,

I have two questions.
I saw there are a lot of algorithms for mris_register. Which one are more precise and has less distortion on sulci pattern?
In initial alignment if I want to rotate the surface with -rotate [ alpha is (ear to ear) beta(Back to nose) ... ]. Am I right?. and if I want that mris_register does not apply any rigid alignment after initial rotation what I have to do?

Thanks
Rouhi


On Thu, Aug 11, 2011 at 9:25 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
What format is the attachment in?



On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi <roohy466@gmail.com> 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



<subject_1&2_side_view.odp>



--
With Best Regards
           Rouhollah Abdollahi