Hi Nicholas
I'll cc Matti Hamalainen who should be able to help you, as he does this kind of thing routinely within his MNE package.
cheers Bruce
On Wed, 20 Aug 2014, Nicholas Heugel wrote:
I am running analysis where I am taking fMRI data using Freesurfer to project it onto the cortical surface and load it into Brainstorm to use as a constraint on the source reconstruction. I am able to do all the steps just fine, the problem I am encountering is that Freesurfer creates a surface with 200,000+ vertices, for the analysis I am running I downsample it in brainstorm to 15,000 vertices to reduce run time. However, when the label file for Freesurfeer gets down sampled it significantly changes how the scouts look. Is there a way to have Freesurfer create a surface with 15000 vertices and then project the volumetric fMRI onto that surface so I don't have to downsample the data? I know there is the function fmris_decimate, which should allow me to decimate targeted files. But I am not sure if I can then use mdi_vol2surf to put the fMRI data onto the decimated surface files, or if I need to have the entire surface file generated from the beginning with only 15,000 vertices. Can I use the recon-all function to define the number of vertices I want, or is that a variable I can't adjust? Any help in the matter would be appreciated.
Nicholas