8000 What to do with profile sampling output? · Issue #116 · nighres/nighres · GitHub
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What to do with profile sampling output? #116

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christopherrowley opened this issue May 30, 2019 · 1 comment
Open

What to do with profile sampling output? #116

christopherrowley opened this issue May 30, 2019 · 1 comment

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@christopherrowley
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I am looking for some help with the file outputs. The "volumetric layering" code outputs what appears to be a correct boundary file, but the depth and layers images appear to be empty. That shouldn't matter too much, as I only need the boundary file for the "profile sampling" module. The "profile_sampling" module outputs a nifti file, but I am not sure exactly what to do with it, or how the data is stored in it. If everything is run with the default 10 layers, how would I extract the 10 sampled surfaces from this file? I'd like this for visualization of the data, and for analysis of the values on the surface. The documentation doesn't seem to have many answers for me on the module (https://nighres.readthedocs.io/en/latest/laminar/profile_sampling.html). Previously using the mipav CBS tools, I would get my surfaces out as VTK files and use matlab scripts to analyze them. Is it possible to obtain these surface files for further matlab analysis?
@piloubazin
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The depth file being empty is a bit weird, did you check that the inputs are good level sets of the surfaces of interest?
For the layer mapping, it's still the same method as CBSTools: the layer mapping gives you surfaces mapped at each cortical depth (so a 4D image with 10 values in the 4th dimension), which you can then project to the .vtk file of your choice (my recommendation: the middle layer of the volumetric_layering turned into a .vtk mesh with levelset_to_mesh).

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