Hi Bruce,
Thanks a lot for the suggestions! Here are some followup questions.
1) The functional volume was PET data and anatomical data have been
processed with Freesurfer. I run the bbregister as:
bbregister --mov PET.nii --s subject_name --reg register.dat --t1
--init-header
It does not register the PET to anatomical images well. Since PET contrast
does not like the typical t1/t2, I am not sure how to set the "--contrast"
argument (already tried to both t1 and t2). Also, as PET and anatomical are
both in native space, not sure how to set the "--init-"
2) Actually, the PET image has been aligned with orig.mgz well (in the
native space) using a in-house method. The registration matrix likes below:
0.992629 0.109294 0.052358 10.4812
-0.102034 0.986829 -0.125525 16.5118
-0.065387 0.119257 0.990708 -23.4735
0.000000 0.000000 0.000000 1.0000
I wonder if there is a way that can convert this matrix to a readable
format for "mri_vol2surf".
3) I tried to run mri_vol2surf (using a --regheader option as pet.nii and
orig.mgz already aligning well) as:
mri_vol2surf --mov PET.nii --hemi lh --regheader subject_name --o
lh.pet.mgh. But the results does not look right.
Any suggestions for these questions would be very appreciated!
-Liang
On Fri, Dec 5, 2014 at 5:40 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Liang
>
> try bbregister.
>
> cheers
> Bruce
>
> On Fri, 5 Dec 2014, Liang Wang wrote:
>
> Hi Experts,
>>
>> At subject level, I want to convert a functional volume (in a subject's
>> native space) to this subject's native surface. The functional volume has
>> been registered to this subject T1 images in native space. I know
>> "mri_vol2surf' would do the job but unsure how to generate the
>> registration
>> matrix for --reg option. I appreciate any suggestions.
>>
>> Thanks
>> -Liang
>>
>>
> _______________________________________________
> 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.
>
>
_______________________________________________
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.
