Describe the feature you'd like to see
Given the length to generate some of the tests, would be a good idea to split the tests up (re: see snakebids)

Describe the feature you'd like to see
At some version of Slicer, I believe the coordinate system either switched or could be toggled to be LPS or RAS. We had previously implemented something to handle this in the afids-validator, reading in the coordinate system and flipping the coordinates as needed when reading in files.

We should probably implement it here too.

Describe the feature you'd like to see

Internal validation of AFIDs files upon loading. Some further discussion should be had here as well. During the sprint, the use of this for non-standard fiducials was discussed. I think if that is the case, we can have something similar to pybids where we have this validation implemented and performed by default, with the option of turning it off. Open to other suggestions.

From #20, this is PR to separate additional features that we would like to see included for plotting in 3D:

• Overlay of a surface mesh of brain
• Inclusion of segmentations (e.g. ventricles, STn, etc.)
• Intersection planes if nifti is provided

Describe the feature you'd like to see

Computation of metrics between AFIDs (e.g. AFLE).

Describe the feature you'd like to see
With this library being type hinted, pyright would be a helpful addition.

Describe the feature you'd like to see
We should prioritize including some simple installation instructions to the README for now (for both users and developers).

Describe the feature you'd like to see

Updating the methods for handling transformations between world and voxel coordinates.

Describe the feature you'd like to see

To enable sampling around a fiducial for various ML approaches. Would need to think how testing for this performed.

Coodinate system defaulting and notation

Switch convention such that 0 = RAS and 1 = LPS

Additional context
Slicer has moved to defauling coordiantes in LPS convention now (4.10 onwards)

Describe the feature you'd like to see
Had some discussion about dropping some metadata that was irrelevant for the usage of afids_utils. Namely, storing the slicer_version does not provide any added benefit, and actually is only relevant to .fcsv files. Open to hearing people's thoughts before dropping this though.

I am trying to load an fcsv file which has some "jumbled" ordering of AFIDs (i.e., AFID 19 placed at 4th position but still contains the correct label). The load method seems to fail due to that (see attached screenshot). Perhaps creating a load method with some agnostic features to the loaded file may be a good thing to include.

Describe the feature you'd like to see
Currently the afids_utils.io.afids_to_fcsv function writes a (32, 3) NumPy array to an fcsv file based on the template. The 32 AFIDs expected in this function is not a hard rule and is based off of the number of AFIDs expected in the provided template. In the future, we may expect a different number of AFIDs due to subsetting of existing fiducials or even for different species.

To that end, a couple of checks should be implemented in this function to:

1. Confirm that the number of AFIDs (e.g. 32) matches the number of expected number of AFIDs in the template
2. Check that the second dimension is equal to the 3 expected spatial dimensions (x, y, z)

Describe the feature you'd like to see

• Orthogonal planes with points highlighted
• Summary plots
• 3D interactive
  • Glass brain
  • Optional intersecting planes (similar to slicer) if nifti is provided
  • Inclusion of segmentations

Describe the feature you'd like to see

Add a last step that runs poetry publish to publish package to PyPI

Describe the feature you'd like to see
Make use of the sphinx extension autodoc_docstring_signature (or whichever extension is relevant) to automatically pick up type hints and drop the repeated type hint that is manually written in the docstrings.

Describe the feature you'd like to see

Create a readthedocs and incorporate docstrings of existing functions

Describe the feature you'd like to see
Some discussion was had about being able to apply external transformations (e.g. ANTs) to the fiducials.

Additional consideration is whether the afids need to be in a certain coordinate system.

Describe the feature you'd like to see

A similar implementation as to the fcsv handling, but for handling AFIDs saved in Slicer JSON files.

Describe the feature you'd like to see

Fill out the README to be more descriptive about the project. This should include any status / doi badges