You should register the fMRI to the anatomical with bbregister. Run it with --help for more info, also see the wiki tutorial on fMRI integration.
You can then sample the time series to the surface with mri_vol2surf
doug

On 4/1/12 1:52 PM, Kaveh Kohan wrote:

Hi FreeSurfer Users,

I am new to the Freesurfer, I have a question regarding mapping of the resting state fMRI time courses on the cortex area. I apologise in case my question is naive. please bear with me:

Is it possible to have time-courses sampled from cortex? I mean how can I get corresponding time-course for each vertex on the cortex ? I know that FreeSurfer can produce mask for cortex are but I would like to have time-courses on the flattened (2D) map; ie assuming that cortex is flattened, each pixel of the 2D flattened image which resides in the cortex (I guess it corresponds to a vertex on the cortex manifold?) is time-series.

I have ran recon-all on the T1. All of those operation were done using a third party packages that uses freesurfer namely CMTK (http://cmtk.org). I do not exactly know how to use "bbregister" to register the parcellation on the resting-state fMRI image?

I would be thankful if you can help.

Thanks
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