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?
- 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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