Mathieu Guay-Paquet

Deal with nibabel's deprecation of `get_header` and `get_data`

1

`sct_create_mask` generates a couple of deprecation warnings, coming from how we use `nibabel`: ``` .../spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:227: DeprecationWarning: get_header method is deprecated. Please use the ``img.header`` property instead. * deprecated from version:...

I thought about `__all__` as well, but (apart from any further subtleties) we don't have an explicit list to give it, since we're importing `*`. We're definitely not being pythonic...

Re-decentralize the contributing guidelines

1

As discussed in #3644, quoting @joshuacwnewton: > So, just to give some context, here. About 2 years ago, each NeuroPoly project (SCT, ivadomed, shimming-toolbox, axondeepseg, etc.) had its own guidelines....

@mchen1110 is running into a file permission issue when trying to run `sct_run_batch` on Windows, at the step where it tries to make a copy of the script to run:...

[FIX] Re-align the text and the schema for filenames in derivatives

4

I initially set out to add the `desc` entity to the filename templates for segmentations (in [the 'Segmentations' subsection](https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#segmentations)), since the BIDS spec says [here](https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html) that: > When necessary to...

Switch to using mean magnitude for output `moco_params.tsv` file used for QC

4

The purpose of this QC file is to identify the amount of motion in each volume (that is, at each time point), so that motion-related fluctuation in the signal can...

With the last-minute fix from #4287, color codes will ~start to~ appear in the text log files created by `sct_run_batch`, as a compromise, so that they can also appear in...

Prototype sub-commands for the `sct_deepseg` CLI

1

As discussed in the [2023-11-30 SCT dev meeting](https://docs.google.com/document/d/1ItApJQfajO2lRzOU2yenWbeRg6alfsdut3J4AVVdo78/edit#heading=h.sl17y9esapii), we would like to improve the command-line interface for `sct_deepseg`. The biggest suggested change is: * Using sub-commands (like `git`, which has...

Restructure QC report code

1

This is a draft PR, to get early feedback on a proposed code structure for the QC report generation code. Currently, it only contains a proof of concept for `sct_register_multimodal`...

This issue is to keep track of some ongoing work for refactoring the QC report generation code in SCT. The goal is to make it much easier to fix bugs...