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