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
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?
- 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 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
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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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Shantanu Ghosh