not easily. Why would you need to do such a thing?
On Fri, 12 Aug 2011,
Rouhollah Abdollahi wrote:
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 <fis...@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
<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
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
--
With Best Regards
Rouhollah Abdollahi
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
