Dear freesurfer experts,
I have .sig maps of cortical thickness, curvature and sulcal depth measures from my dataset (two groups: patient, control). I have the following questions:
1) I want to overlay all three maps simultaneously on an average subject created from all subjects' brains, with different color maps. Which command will do this?
2) Register all ?h.thickness datasets to mni152 instead of mni305/fsaveage, convert the files to .mnc/.obj format, and read in Matlab. In this step, do I have to convert the native ras coordinates too? If I want to use bbregister for this step, can you specify the commandline to do this?
3) I want to compute vertexwise expansion/contraction for local surface area, by a) calculating total surface area of all faces connected to a vertex, and then multiplying it with corresponding curv and sulc of that vertex, and b) comparing the result in 3a) with the warpfield from the registration form step 2) above. Or is there something I am missing here?
Also, for 3a) how do I get the correct set of triangles for each vertex?
Thanks in advance, Shantanu