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 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?

Thank you very much,
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