On 01/13/2013 09:17 AM, Shantanu Ghosh wrote: > Dear Freesurfers, > I posted the questions yesterday but received no answer so far. I really > need help with this. Posting thsi again. > Thanks in advance, and sorry for the double posting. > S > > On Sat, January 12, 2013 2:02 pm, Shantanu Ghosh wrote: >> Dear freesurfer experts, >> >> I have .sig maps of differences in 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? make_average_subject can be used. I'm not sure what you mean by having all 3 maps simultaneously. A vertex cannot be simultaneously two different colors. >> >> 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? I don't know what you mean by this. You can run mni152reg to compute a registration matrix. >> >> 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 The ?h.area file has the average area of a vertex. You can use fscalc to multiply that by ?h.curv. >> 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 >> >> >> --
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