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March 08, 2022 01:41PM
I'll try to answer some of these questions:

3dVol2Surf is to move data from the volume into the surface for data in the same space.

I don't understand this:
If it is possible to do it with my WARP files, what would be the correct command line?

You can make spec files with quickspec. The spec files are fairly straightforward text files, so you could simply edit them too.

For surface area, you could use the triangle output from SurfaceMetrics. The sum of all the triangle areas is the total surface area. Alternatively, SurfMeasures gives several surface output values on a node-wise basis. The stdout includes the total surface area. The "n_area_A" gives the area associated with each node (total triangle area/3) and the average area of the triangles associated with each node (if 6 triangles are are associated with a node, then the total area of the triangles/6). Summing across the n_area_A column should give you something very similar to the total surface area presented to the stdout in the terminal. See this old discussion for the differences among these options.

[afni.nimh.nih.gov]

So if you do something like :

SurfMeasures -info_area -spec tempqs.spec -surf_A mysurface.gii -out_1D testout.1D \
-func n_area_A -func n_avearea_A -func n_ntri

You get output in the terminal that says "total area 0 = nnnn.n"

The text file, testout.1D, looks something like this:

# nodes n_area_A n_avearea_A n_ntri
# ---------- ---------- ---------- ----------
0 0.291586 0.145793 6
1 0.203118 0.121871 5
2 0.251291 0.125645 6
3 1.023988 0.438852 7

You can sum the n_area_A column with this command where the output should be very close to the total area above:
3dTstat -sum -prefix - testout.1D'[1]'\'
nnnn.n

Also note that the product of the last 2 columns (n_avearea_A*n_ntri) divided by 3 is equal to the n_area_A column.

Because SurfaceMetrics uses triangles and not nodes, they add up more directly. The total area of the triangles should be same as the surface area computed by averaging around nodes.

SurfaceMetrics -area -prefix testSM.1D -i mysurf.gii
mv testSM.1D.area testSM.1D
3dTstat -sum -prefix - testSM.1D'[1]'\'
nnnn.n
Subject Author Posted

Surface measures on CHARM

Doughboys February 23, 2022 03:48PM

Re: Surface measures on CHARM

Daniel Glen February 23, 2022 07:01PM

Re: Surface measures on CHARM

Doughboys March 08, 2022 11:13AM

Re: Surface measures on CHARM

Daniel Glen March 08, 2022 01:41PM

Re: Surface measures on CHARM

Doughboys March 18, 2022 03:36PM

Re: Surface measures on CHARM

Doughboys April 04, 2022 12:19PM

Re: Surface measures on CHARM

Daniel Glen April 04, 2022 01:16PM



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