Add command line for computing CSF and intracranial masks#43
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finsberg
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Looks good! I think we should also add some tests which test this on the gonzo dataset. Do we have the csf masks generated in the dataset? Also it might be good to add a bit more information about the input image to the csf mask parser. Right now it sais "Path to the input NIfTI image", but can this be any input image. From the docstring in compute_csf_mask_array it looks like it should be either T2w or Spin-Echo?
Similar to the other PR (#41), I think it is better to save the output file in the dispatch function. That way, we can get rid of the output argument to the functions and the functions does only one thing.
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…from csf segmentation (not csf mask)
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Indeed. we have the csf/intracranial masks in the gonzo dataset, I have now added the corresponding tests and also some dispatch tests to be consistent with what is done in I also updated the "help" message describing the input for the CSF mask, and removed the |
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