Julien Cohen-Adad

Discussing strategies to backup IDE-related config files

1

For developers using IDE, config files are useful to keep and backup. Eg: `.vscode/launch.json` for VScode (to test CLI), `.idea/` for Pycharm. I see such files in other repos sometimes....

When using `sct_crop_image`, if the image and mask are not in the same space (same qform, same resolution), the cropping is not done as expected. A suggestion is to check...

Add flow calculation to `sct_compute_flow` CLI

2

I'm working on a project where flow is to be computed from [VENC](https://mriquestions.com/what-is-venc.html) sequence. It would be nice to have a function to do that in SCT. More details in...

Add the possibility to add comments associated with a flag 'QC'

6

When reviewing QC reports, in some cases we might want to add some comments (eg: "oversegmentation on slices 3-4"). We should consider adding a way to add a comment. Some...

[This article](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/nbm.5052) came to my attention today. Shimming Toolbox and qMRLab are cited, but SCT is not. I suggest adding SCT to the [OSI list](https://gitlab.com/osii/cab)

SCT Course: Weird bullet formatting when creating a new slide from the existing template

4

when creating a new slide using the template, the numbering font size is screwed up: https://github.com/spinalcordtoolbox/spinalcordtoolbox/assets/2482071/33ee4dd1-48ab-421d-807f-5f1157193fcd and when matching the font size, the numbers are no more aligned with the...

Confusing existence of `PAM50_label_body.nii.gz`

3

### Description In `sct_register_to_template`, the vertebral labels (ie: single label per vertebral body) is generated from the file `PAM50_levels.nii.gz`: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/792a155fdb55aaae8096a2d6b32874d1a98fcc13/spinalcordtoolbox/scripts/sct_register_to_template.py#L424-L428 However, the folder `PAM50/template` and includes a file called `PAM50_label_body.nii.gz`,...

Access to source code of optic functions

6

## Context The source code (developed by @sdika) for binaries `isct_spine_detect` and `isct_train_svm` has been unaccessible by the SCT team until now. SCT's team has now access to the code...

Improve the performance of `sct_fmri_moco`

2

Based on discussions with a few researchers (notably Rob Barry), it looks like AFNI is great for aligning spinal EPI time series, so we should get inspirations about what specific...