Joshua Newton

## Description This PR adds a `-volumewise` argument to automate the steps described in issue #4181: > 1. Run `sct_image -split t my-image.nii.gz` to generate a separate file for each...

Allow multiple `sct_maths` operations to be run sequentially on an image in one command

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## Description This PR allows users to provide multiple arguments and have them be run sequentially, in the order provided. Example: ``` sct_maths -i im_0.nii.gz -add im_1.nii.gz -mul im_2.nii.gz ```...

## Description Quick, straightforward refactoring PR. Check commits for more details. :) I could have definitely gone further with docstring/comment changes? The "center of mass" code is a little unclear...

Track upstream packages to determine when we can upgrade to `numpy==2.0.0`

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e.g. https://github.com/spinalcordtoolbox/spinalcordtoolbox/actions/runs/9546561946/job/26309700294 Release notes for `numpy==2.0.0`: https://numpy.org/devdocs/release/2.0.0-notes.html List of upstream issues tracking incompatibilities (for quick status monitoring for when we can try upgrading to `numpy==2.0.0`): - https://github.com/matthew-brett/transforms3d/issues/66 - https://github.com/scikit-image/scikit-image/issues/7445 -...

`sct_download_data` deletes the contents of the output folder by default, which is dangerous when combined with `-o`

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I wanted to download `sct_example_data` to my PWD, so I ran: ``` sct_download_data -d sct_example_data -o . ``` Which then proceeded to irreversibly delete everything in my PWD. :facepalm: I...

The following points were brought up in the 2024-06-13 SCT Meeting: - People are attempting to use `sct_deepseg_lesion` for non-MS lesions (e.g. SCI) - People are unaware of the other...

Provide better instructions when Windows username contains spaces

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- SCT installer fails if paths contain spaces - But, if the username contains spaces (e.g. `Firstname Lastname`), then all paths will contain spaces. - Other paths on `C:\` exist,...

I got a failure notification on master the other day: - [38m 46s](https://github.com/spinalcordtoolbox/spinalcordtoolbox/actions/runs/9382948813/job/25835620060) - many failures - [21m 40s](https://github.com/spinalcordtoolbox/spinalcordtoolbox/actions/runs/9382948813/job/25845676211#step:9:509) - no failures I don't know how frequent this will be....

A small refactoring observation that I noticed while lazy-loading the `dipy` imports in #4490. ---- Interestingly, the noise `sigma` calculation is different for the `nlmeans` method depending on which entry...

**Is your feature request related to a problem? Please describe.** We have a model that produces a "soft" (i.e. not binary) segmentation output. In our preprocessing steps for the input...