Hi Bruce,
Thanks for your response. A couple of follow-ups:
1) Is using bbregister usually better than using FLIRT? After all, isn't it simply an affine transformation? 2) If I want to move my parcellation from MNI_2mm space to subject native space, shoud I use the MNI_2mm template as my input/movable volume and my SubjID as my subject? 3) What about cvs_register? Will I get a better registration outcome if I use this as opposed to bbregister, followed by mri_vol2vol?
Thank you very much, Bruce!
-- Marcelo
On Sat, Oct 11, 2014 at 5:04 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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