Julien Cohen-Adad

Function usage requires manual refresh to appear

7

### Description When loading the sct_plugin script in FSLeyes, the first tab (propseg) shows the usage of the function, but the other tabs don't by default. It requires manual action...

We should provide a satisfactory solution for every users working with thoraco/lumbar data. Currently, registration to the template is not easy. Some thoughts: - Create a cauda equinea label in...

Add microstructure atlas to PAM50

4

Data are here: https://osf.io/8k7jr/ Todo: - bring the atlas in the same coordinate space as the PAM50 - maybe generate a subsampled version? (or in addition to?) - update the...

Make AtlasRat downloadable

1

Source of the atlas is here: https://osf.io/g7kx8/ What needs to be done: - organize files into template/ and atlas/ folders to be compatible with `sct_register_to_template` - bring AtlasRat Paxinos atlas...

Use bot to list contributors

12

This looks useful: https://allcontributors.org/ Example of how it looks like: https://github.com/datalad-datasets/ohbm2020-posters#-contributors

Possible deprecation

1

```bash /Users/julien/code/sct/python/envs/venv_sct/lib/python3.7/site-packages/skimage/morphology/misc.py:39: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0.Please use `footprint` instead. return func(image, footprint=footprint, *args, **kwargs) ```

Add to documentation: registration between CT and MRI

1

Here's the relevant example: https://forum.spinalcordmri.org/t/registration-between-two-segmentations-multimodal/818/4?u=jcohenadad we could add it as a "demo" either on our tutorial, and/or on our course slide material, and/or somewhere else...? But i think it is...

Make it possible to upload a YML file to resume a long QC analysis

7

## Context When reviewing QC reports, users manually label processes with 'pass', 'fail' or 'artifact'. If they need to stop working temporarily and close their browser, their work is lost....

### Description As noted by @mariehbourget [here](https://github.com/ivadomed/model_seg_ms_mp2rage/issues/43#issuecomment-1022348177), there was a recent change in ivadomed that implied that 3rd party software should _not_ rely on `target_suffix` to name predictions. A possible...

Input image is overwritten if no output file is specified

3

### Description Running this innocent command: ~~~ sct_image -i image.nii.gz -setorient RPI ~~~ Will overwrite the input image 😬 . We definitely want to avoid this behaviour, and instead set...