Joshua Newton

First, thank you for taking the time and effort to create this useful template! :) ----- I noticed for base_model.py and base_trainer.py, you are using the `abc.abstractmethod` decorator from the...

> **Last updated**: 2021/12/12 This issue is used to keep track of progress on feedback/ideas received from the 2021 SCT Course. ### Slides - [x] https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3614 - [x] https://github.com/spinalcordtoolbox/sct_tutorial_data/issues/7 -...

This issue was created from a bullet point that was originally written down in: * https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3612 I'm pulling it out to clean up the issues in the SCT repo.

`find_and_sort_coord` function handles empty-array input errors in an unclear way

6

Error reported by user on the forum: https://forum.spinalcordmri.org/t/valueerror-when-using-register-to-template/867/2  Will update with more information if/when the user provides an image to try to reproduce the issue with.

Scaling issue with nibabel.save() when header datatype is `int`, but array datatype is `float`

17

### Description > This is a follow-up to #3229. A bandaid fix was applied in #3230, but the root cause is deeper. If an image has non-zero float values, and...

Move `sct_merge_images` functionality into `sct_label_utils`

2

_Originally posted by @jqmcginnis in https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3828#issuecomment-1178914060_ > Another idea might be to include the `sct_merge_images` in the `sct_label_utils`? If label fusion is the primary use case, perhaps it would be...

Replace existing `run_proc` calls with `sct_script.main()` calls

2

About a year ago, we modified our CLI scripts so that their `main()` functions could be called in-code. For example: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/c5f194410605dd9c5035d704e1656930830a9cdc/spinalcordtoolbox/scripts/sct_image.py#L557 However, before we had this capability, we would use...

Add QC reporting to `sct_deepseg_lesion`

5

Additional context given by @jcohenadad: > note that this particular QC is quite tricky (although not impossible)-- because lesion seg could happen on sag or ax images, and the QC...

Add support for Python 3.8 and 3.9 by 2023-06-27

4

https://github.com/neuropoly/spinalcordtoolbox/pull/3361 adds support for Python 3.7. However, ideally we should be testing our package against Python 3.7/3.8/3.9 so that we can be aware of any incompatibilities far ahead each version's...

Improve `sct_label_vertebrae` using a deep learning-based approach

13

## Context The `sct_label_vertebrae` function currently works by using a C2-C3 disc detector, then using a template-matching, similarity measure-based approach to identify discs. In other words, it uses traditional computer...