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:
- 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.
- 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.
- 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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