Julien Cohen-Adad

Optimize threshold to render CSA contrast-agnostic

1

After ivadomed's softseg is implemented, we could derive a project where we optimize threshold (or segmentation ground truth) across contrasts in order to minimize inter-contrast variability in CSA.

Cosmetic/UX improvements on the PyQt viewer for centerline manual labeling

2

After #3175, the following (minor) improvements are suggested: - Fix text overlapping on the image: this sometimes happen depending on the resizing of the figure or the zoom on the...

As done for sct_deepseg_sc

### Description When listing the labels ID using an atlas that is _not_ located at `label/atlas/`, the command crashes: Terminal output ```console julien-macbook:~ $ sct_extract_metric -list-labels -f ~/code/sct/data/PAM50/atlas/ -- Spinal...

Discrepancy between sct_qc and centerline results

5

Version: SCT dfd51cd39921a592f062b326a1d680e43b8ca5e0 Data: sct_testing_data/t2 When running: ~~~ sct_get_centerline -i t2.nii.gz -c t2 ~~~ I obtain a correct centerline, with only **one** pixel per axial slice. Example here for the...

doc 4. Computing shape metrics for PAM50-registered data

1

In principle, it is not necessary to register data to the PAM50 for computing shape metrics. Also, many users will look for the keyword 'CSA'. So i would suggest to...

make videos for documentation

5

make Youtube channel - [ ] Installation: show webbrowser, miniconda, download package, install, check_dependence, testing - [ ] batch_processing: copy/paste approach

`-param type=label` cannot be used in `sct_register_to_template` because the `ilabel` and `dlabel` flags do not existe in `sct_register_to_template`

2

This registration option is possible with `sct_register_multimodal` but not with `sct_register_to_template` because the `ilabel` and `dlabel` flags do not existe in `sct_register_to_template`. Solution: - introduce `ilabel` and `dlabel` flags

It is unclear how to list subjects to include for the flag `include_list` when providing a yml/json file, so let's add it in the usage under flag `-config`: ~~~ include_list:...

### Description Usage says: ~~~ -method {optic,viewer,fitseg} Method used for extracting the centerline. - optic: automatic spinal cord detection method - viewer: manual selection a few points followed by interpolation...