Hi Bruce,

I'm chiming in because I've been having a similar issue with the method you mention above. Though, my goal is just to move the surface rendering into the subject's native space using tkregister2 and mri_surf2surf as suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

The problem I ran into is that the surface output from that procedure looks fine overlaid on the subject's native T1 in freeview (even if the original T1 was in LAS orientation). However, if I view the surface in any other viewer (e.g., in matlab using surf() or tripatch()), the surface is flipped left from right, and the frontal pole is facing down (what is usually ventral). I'm assuming freeview applies some transformation to orient it correctly, but I'm stumped there. 

I was exchanging with Doug Greve about this and we couldn't figure it out. Any advice you might have is much appreciated.

Thanks for your help!

-zack

On Sat, Oct 11, 2014 at 2:04 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Marcelo

you can use bbregister to register the surfaces to another volume, and
mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to
apply the volume transform)

cheers
Bruce
On Sat, 11 Oct 2014, Marcelo Mattar wrote:

> Hello,
> I'm new to Freesurfer, and I'm lost in something that I believe is very
> basic. I have a parcellation of the brain in .nii format that is currently
> in MNI space (2mm). I would like to move this parcellation to subject native
> space, so that I can extract the BOLD timeseries from each region of the
> parcellation.
>
> I understand that an option I have is to simply use FSL tools such as FLIRT
> or FNIRT and move the parcellation file to subject space (using nearest
> neighbor interpolation). However, given that I have reconstructed the
> subject's anatomy to the surface space, I believe I can do a better job that
> just an affine transformation.
>
> What should I do in this case?
>
> 1) Is there any freesurfer tool that would allow me to register a volume to
> another volume, but aided by surface information?
> 2) If so, what steps should I follow to extract BOLD timeseries for each
> subject from the parcellation regions?
>
> Thank you very much,
>
> --
> Marcelo Mattar
> University of Pennsylvania
>
>
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