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 <roohy...@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 <fis...@nmr.mgh.harvard.edu>
wrote:
Try using fsaverage as the trgsubject
Cheers
Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy...@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
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