Ali Khan

Update indexer to treat .zarr as files not dirs

1

Microscopy file formats were recently updated in the standard to include ome-zarr, which are stored in a directory suffixed with `.ome.zarr`. https://bids-specification.readthedocs.io/en/stable/modality-specific-files/microscopy.html#file-formats This however doesn't work with pybids currently, since...

ENH: Dealing with gradient non-linearities

3

For gradient systems with significant non-linearities (e.g. connectome scanner, some 7T head-only systems), it is important to account for these as they not only lead to spatial distortion, but also...

Incompatibility with Poetry?

3

Hello, The dependency solver seems to go on an infinite loop when trying to add `ome-zarr` to a poetry project. Can be reproduced even with just ome-zarr as the only...

Add DAG generation to a github action

1

I started making one awhile ago, but now with the new subgraph dags (added in #209) would be good to revisit this automation: https://github.com/khanlab/hippunfold/blob/118693a02bdc286bc7fd50568298c480d4f1fc35/.github/workflows/dags.yml

Total Intracranial volume estimates

2

TIV is a necessity for volumetry so would be nice to include an estimate in the output volume TSV files. Could use the freesurfer approach which extracts it from a...

add better support for conda

2

Currently we are using poetry for dependency management, but could be nice to also add direct support for conda (e.g. avoiding problems as in #168). Could: - create a conda...

Add an option in generate_inputs to ignore files from pybids parsing?

1

## The problem Would be useful to be able to ignore specific files when parsing a bids dataset. In my case, it is because I'm now parsing some datasets that...

Maybe have a way to support this kind of usage: Very simple single image -> output folder CLI (kind of like recon-all, except not implicitly using env var for subjects_dir)...

anterior-posterior subdivisions option

2

Add a rule and CLI option for performing dynamic subdivision of the atlas into A-P subdivisions. Values could be '1', 'hbt', 'uhbt' or '#' (any number), where hbt/uhbt will result...

Snakebids create docs

3

## The problem The docs for the CLI (app and snakemake) don't build properly since the snakebids isn't in the requirements.txt for the docs. Looks like simple fix is to...