Thanks for the reply. I might have been misleading in my initial description. I have my functional data in .nii.gz format coregistered to a structural .nii.gz using FSL Feat. I subsequently ran the structural through the recon-all pipeline. With that setup, I am currently aware of how to programmatically (using matlab) access the functional data in .nii.gz format, but not how to query vertices. At this point it's not entirely clear to me how I would use mri_vol2surf to be able to access the spherical data. Does mri_vol2surf output a transformation matrix of some sort that I can apply like a Feat registration to my functional .nii.gz? If instead of trying to access the data in .nii.gz, I should access the vertices in some freesurfer format, how would I a) access a particular vertex using matlab b) use mri_vol2surf to map my functional data onto the surface? For b) I'm just not sure how I would tell mri_vol2surf that it needs to register to the structural using Feat's registration before registering to the sphere or other. Thanks again.

Best Regards, Luis ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, June 07, 2012 8:21 AM To: Luis R. Piloto Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Export Functional Data Overlayed Onto Sphere

Hi Luis

if your functional data is mapped onto the surface (i.e. with mri_vol2surf) then it is already on the sphere. All the surfaces for a given subject's hemisphere are topologically equivalent, so you can simply look up the same vertex index on the ?h.sphere (for the metrically optimal spherical coordinate) or the ?h.sphere.reg (for the spherical coordinate that is in register across subjects).

cheers Bruce

On Thu, 7 Jun 2012, Luis R. Piloto wrote:

Hello,

I've specifically adopted Freesurfer for its ability to map a brain into a sphere. I've ran a subject's structural data through the recon-all pipeline using the -all option. With this reconstruction completed, I'd like to overlay functional data on the sphere. More specifically, I'd like the ability to programmatically query a point on the sphere and get the corresponding activation. Is there a reasonable way to do this within the Freesurfer pipeline? I already have the ability to programmatically query my initial functional data, so it would suffice to get a transformation matrix from my structural data to the spherical coordinates. Any thoughts/suggestions would be appreciated.

Regards, Luis Piloto _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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