Sorry. I meant to do that.

---- Original Message ---- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Arash Nazeri arashnazeri@aol.com Sent: Wed, Oct 23, 2013 8:25 am Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file

Hi Arash

can you cc the list on this type of email so that others can answer? Particularly Matt Glasser! I suspect that they have already run bbregister, but I'm not sure.

cheers Bruce

On Wed, 23 Oct 2013, Arash Nazeri wrote:

Hi Bruce, Thanks for your response. I think this will do the trick generally, is it also possible to apply mri_vol2surf to the Human Connectome Project preprocessed files, or should I rerun the recon-all? In the HCP dataset, the surface files are in the gifti format and the diffusion images are already registered to the structural volumes. Based on the documentations it seems that mri_vol2surf is hard-wired for outputs generated from recon-all.

Cheers, Arash

-----Original Message----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Arash Nazeri arashnazeri@aol.com Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tue, Oct 22, 2013 10:17 pm Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file

Hi Arash Yes. Register the surface to the volume with bbregister, then use mri_vol2surf to do the sampling Cheers Bruce

On Oct 22, 2013, at 12:13 PM, Arash Nazeri arashnazeri@aol.com wrote:

  Dear all,

I'm new to the freesurfer. I want to project surrounding cortical voxel values (intensities) from a given map (e.g. mean diffusivity map in a nifti format) to a surface file (e.g. mid-cortical surface in a gifti fromat) to generate scalar maps like ?h.thickness for group-wise statistics. Can this be carried out using freesurfer commands?

Cheers, Arash

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