jcreinhold/intensity-normalization

No documentation for brain_mask in intensity_normalization.normalize.fcm.find_tissue_mask

goyal-aman opened this issue · 3 comments

goyal-aman commented

📚 Documentation

To normalize the T1 Weighted image, using normalize normalize.fcm.fcm_normalize which require tissue_mask for which according to documentation I am using this normalize.fcm.find_tissue_mask in which brain_mask is a required parameter but there is no refrence in documentation that I can find about what it should be.

jcreinhold commented

Hi @goyal-aman. I'm not sure I understand. There is documentation about what the brain_mask argument should be in the docstring. See here.

Can you clarify what you mean?

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goyal-aman commented

Hi @jcreinhold, sorry for not being clear. What I meant was I couldn't find anywhere in the documentation that what should be passed in the brain_mask argument. I am just getting started with brain_image processing. I apologise is question sound dumb.

jcreinhold commented

@goyal-aman No problem. My documentation isn't clear—you're question is good. The brain mask should be a binary array, the same size as the MR/CT image, which is 1 in the voxels/pixels corresponding to the brain and 0 in all other voxels/pixels.

Hope that helps. I am going to close this and factor this into my open issue regarding refactoring the package (#24).

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