Hi Rouhi
you can specify -norot to disable the initial rotation, but I wouldn't
think that would be a good thing to do. To decrease distortion you would
increase the strength of the metric term using -dist <float>. The default
is 5, so you could try raising it to 10 or 15.
cheers
Bruce
On Fri, 12 Aug 2011, Rouhollah
Abdollahi wrote:
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 <fis...@nmr.mgh.harvard.edu>
wrote:
What format is the attachment in?
On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi <roohy...@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
<fis...@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
<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
<subject_1&2_side_view.odp>
--
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.
