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?
>
> 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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