Re: [Freesurfer] Registering a parcellation from MNI_2mm space to subject native spac

Yes, there is, and there is an adjustment made to the vox2ras so that freeview reads it properly. Still that should not affect the actual coordinates. However, if you want to use another viewer, you have to make sure that the coordinates are consistent between the volume and the surface. Just throwing it into another viewer is surely going to fail. The coordinates will be in tkregister-style XYZ in the target space. Look at our page on coordinate systems to see what that means.

doug

On 10/13/2014 06:28 PM, Bruce Fischl wrote:

Hi Zack

there is a ras2vox transform in the surface file header that I believe freeview uses. I'll cc Ruopeng so he can confirm and give you details

cheers Bruce On Mon, 13 Oct 2014, Zachary Greenberg wrote:

...

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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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