Joshua Newton

Clean up the "Pathology" and "Tools" columns in "studies_citing_SCT"

6

In https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3896, we began displaying statistics graphs from our "studies_citing_SCT" Google Sheets spreadsheet. For example:  But, I noticed in https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3857#issuecomment-1261200743 that there were some issues with the data we're...

Currently, if an error occurs inside `isct_propseg`, we output a fixed error message by default, which may or may not be accurate: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/a685d7f0d8032f9df685a08d22947947ac416e71/spinalcordtoolbox/scripts/sct_propseg.py#L615-L619 To find out the real cause, the...

SCT currently has a file called [`sct_plugin.py`](https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/c26086ec3e779d4f8f025651e46de2f962698d98/contrib/fsl_integration/sct_plugin.py) that gets invoked [via the "Run script..."](https://spinalcordtoolbox.com/user_section/fsleyes.html) option within FSLeyes. This script will create an interface within FSLeyes that allows users to run...

`algo=dl` abruptly stops with no error message when used on internal dataset

4

As discovered in https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3865#issuecomment-1232161658, when the following command is run: ``` sct_register_multimodal -i _VISTA_Lspine_SENSE_20210922113031_2001.nii -d _VISTA_Tspine_SENSE_20210922113031_1901.nii -param step=1,type=im,algo=dl ``` The output of `sct_register_multimodal` abruptly stops when trying to predict using...

Consider renaming `sct_plugin.py` to something that is less misleading

1

FSLeyes has "Load plugin" and "Run script" options. However, `sct_plugin.py` is not actually a plugin, so it's not compatible with "Load plugin". Instead, users must choose "Run script". This is...

Consider replacing custom BIDS parsing code with PyBIDS

1

Currently, we're parsing BIDS-structured datasets ourselves (e.g. we manually check paths for `sub-` and `ses-` prefixes, etc.) https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/956d61e8aec1111a3e3cec71219ce6024705bd0f/spinalcordtoolbox/scripts/sct_run_batch.py#L389-L403 As an alternative, we could use [`pybids`](https://github.com/bids-standard/pybids), which is designed for exactly...

Add option to lower the feed scanning interval in order to make fewer requests

2

**Before you start.** * [X] I have checked the [Common Problems](https://github.com/kickscondor/fraidycat/wiki/Common-Problems) page. * [X] I have searched the issue tracker for a bug that matches the one I want to...

Hi there! I come from a lab that primarily uses `nibabel` over `SimpleITK` for image processing. When using nnUNetV2, we did the following: - Training: `nnunetv2_train` on `.nii.gz` images (no...

The full context is here: https://github.com/adalca/pystrum/issues/9 But, simply importing `neurite` will trigger the issue above: ```python File "/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.8/site-packages/voxelmorph/__init__.py", line 12, in import neurite File "/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.8/site-packages/neurite/__init__.py", line 19, in import pystrum...

SCT employs a number of style checks in its CI workflows: [`check_code_quality.yml`](https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/master/.github/workflows/check-code-quality.yml) But, the CI will only catch these issues once a developer has already pushed changes to their branch,...