Jan Valosek

Change title of "A brief introduction to the bash shell" module

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## Work to be done We can consider removing "bash" from [A brief introduction to the bash shell](https://school-brainhack.github.io/modules/introduction_to_terminal/) module title. Possible suggestions: - "A brief introduction to the shell" -...

Reduce "empty" space between raincloud plots

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Hello! Is there a way how to reduce "empty" white space between individual raincloud plots (highlighted by the red arrow in the screenshot below)? Thank you!

Add T2w dorsal rootlets labels

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This PR adds dorsal C2-C8 rootlets labels for T2w images of 24 subjects. The labels were part of the "[D5 dataset](https://github.com/ivadomed/model-spinal-rootlets/blob/main/training/dataset_creation/D5.tsv)" used for training and testing of the "[M5 model](https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457)":...

Two T1w labels for some subjects

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@NathanMolinier and I noticed that some subjects have duplicated T1w labels: ```console data-multi-subject/derivatives/labels/sub-amu02/anat$ ls -1 *T1w*labels*nii.gz sub-amu02_T1w_RPI_r_labels-manual.nii.gz sub-amu02_T1w_labels-disc-manual.nii.gz ``` ### `T1w_RPI_r_labels-manual.nii.gz` These labels were created in the context of the...

Some subjects have different image and label dimensions and resolution

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Some subjects have different image and label dimensions and resolution. For example, for subject `sub-beijingGE02`, T2w image has different `dim` and `pixdim` than T2w spinal cord segmentation: ```console $ sct_image...

Based on our new [convention](https://intranet.neuro.polymtl.ca/data/dataset-curation.html#derivatives-structure), we can consider renaming of: `sub-amu01_T1w_seg-manual.nii.gz` to: `sub-amu01_T1w_label-SC_seg-manual.nii.gz` We can also consider renaming `derivatives/labels` to `derivatives/manual_labels`. Then, we could omit `-manual` from the file names,...

Poor data quality: MT

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**sub-fslAchieva03_acq-T1w_MTS.nii.gz** **sub-fslAchieva04_acq-T1w_MTS.nii.gz** **sub-fslAchieva05_acq-T1w_MTS.nii.gz** **sub-fslAchieva06_acq-T1w_MTS.nii.gz** **sub-beijingPrisma01_acq-T1w_MTS.nii.gz** **fslAchieva:** Wrong placement (should be centered at C3-C4): --> should remove site from statistics  **sub-balgrist02** Wrong placement  **sub-nottwil03_acq-MToff_MTS.nii.gz**  **sub-nottwil04_acq-MToff_MTS.nii.gz**  **sub-pavia05_acq-MToff_MTS.nii.gz** 

Accidentally pushed; please ignore it.

This PR adds missing `vol_diff` key to [BinaryPairwiseMeasures.measures_dict](https://github.com/Project-MONAI/MetricsReloaded/blob/b3a371503f8417839d67b073732170ac01ed03f7/MetricsReloaded/metrics/pairwise_measures.py#L251) Otherwise, the following KeyError is raised: ```console Traceback (most recent call last): File "/Users/user/code/MetricsReloaded/MetricsReloaded/metrics/pairwise_measures.py", line 1161, in to_dict_meas if len(self.measures_dict[key]) == 2:...

Automatically compute midsagittal tissue bridges

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## Checklist #### GitHub - [x] I've given this PR a concise, self-descriptive, and meaningful title - [ ] I've linked relevant issues in the PR body - [x] I've...