Julien Cohen-Adad

There is a way to embed googlesheet graphs as HTML's iframe, so I am wondering if we could do that in a sphinx-built page? If so, it would be neat...

OSError: Too many open files when running moco on large files

2

When running `sct_fmri_moco` in large files with hundreds of volumes, the function crashes (see below). Note: this issue would likely occur on `sct_dmri_moco` as well. To be tested. ~~~ Merging...

Poor handling of case where center of mass of the label image is outside of the labeled region

2

### Description It seems like if C2-C3 is wrongly detected and has a bunch of discs above, then the function will iterate and eventually go through negative discs, which seems...

currently the flag -mask-weighted doesn't seem to do what it is supposed to do. Example below from sct_testing_data: ~~~ sct_extract_metric -i mtr.nii.gz -f mt1_seg.nii.gz -mask-weighted mt1_seg_modif.nii.gz -o mtr-w.csv sct_extract_metric -i...

SCT installation fails without read permissions on `~/.bash_profile`

2

### Description When there is no read permission on the .bash_profile (or equivalent), the installer throws: ```console julien-macbook:~/code/sct $ ./install_sct ******************************* * Welcome to SCT installation * ******************************* Checking OS...

PAM50 atlas warped to the subject's space gives corrupted values

4

### Description This issue was originally reported here: https://github.com/sct-pipeline/gm-challenge/issues/77 The white matter atlas is supposedly encoded between 0 and 1. After estimating warping fields between the subject's space and the...

Mention in the usage that the function works with the `-ses` subfolders

1

It is unclear that `-ses` subfolders are covered with this function.. I suggest adding this in the usage. Maybe as examples of how the folders should be organized Related issue:...

As of SCT v5.4, whenever a `ses-` folder is present under a `sub-*` folder, it will consider it and aggregate subject and session, eg: `sub-01/ses-01` and use this instance inside...

Discrepancies in `batch_processing.sh` results between Linux and macOS

2

Following on https://github.com/neuropoly/spinalcordtoolbox/pull/3050, which ensured intra-OS reproducible results for `batch_processing.sh`, we still observe slight discrepancies across OSs. Example, from https://github.com/neuropoly/spinalcordtoolbox/releases/tag/5.0.1: **Linux:** ~~~ mt/MTR(WM): 54.38365862512906 dmri/FA(CST_r): 0.775626536503328 dmri/FA(CST_l): 0.7800112277757334 ~~~ **macOS:**...

Have the possibility to include a YML file to exclude subjects

2

For reproducibility, it would be nice to be able to input a YML file when running `sct_run_batch`. For example, after QCing results, realizing that some subjects have strong artifacts, we...