Jan Valosek

Improve moco for interleaved data

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## Description This PR tries to address issues with motion correction of dMRI data acquired in interleaved mode. Original issue - https://github.com/neuropoly/spinalcordtoolbox/issues/2637 Based on recommendation from https://github.com/neuropoly/spinalcordtoolbox/issues/2637, I implemented `-interleaved`...

[ENH] Add example dataset for MRI chunk entity

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This PR adds an example dataset for the MRI chunk entity. The "chunk" entity is added to the MRI datatype in https://github.com/bids-standard/bids-specification/pull/1586. Note that I intentionally did not [truncate](https://github.com/bids-standard/bids-examples/blob/master/CONTRIBUTING.md#how-to-truncate-data-files-to-0kb) the...

Can I convert nnU-Net pytorch model to MLX?

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Hi all! Is it possible to convert a medical image segmentation model trained using the [nnU-Net framework](https://github.com/MIC-DKFZ/nnUNet) and stored as a `.pth` file into an MLX compatible format? Thanks!

Broken link in `sct_register_to_template.py` help

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The link in `sct_register_to_template.py` help points to a no longer existing page: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/44587d4cb293e04e635e17fe56137a0c4aa28f8f/spinalcordtoolbox/scripts/sct_register_to_template.py#L122 The `vertebral-labeling` section was moved out from `registration-to-template` in https://github.com/spinalcordtoolbox/spinalcordtoolbox/commit/5b9f2451f40f5e45a3c04d2a9826f34b452d19e8.

`sct_process_segmentation` always uses the `'Slice (I->S)'` column regardless of the input orientation

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### Description The [compute_shape()](https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/764aa9a3313b5d949b5117ed05b3b84a06737066/spinalcordtoolbox/process_seg.py#L25) function used by the `sct_process_segmentation` script reorient an input segmentation to RPI (Right-Posterior-Inferior) before computing shape metrics: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/764aa9a3313b5d949b5117ed05b3b84a06737066/spinalcordtoolbox/scripts/sct_process_segmentation.py#L423 https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/764aa9a3313b5d949b5117ed05b3b84a06737066/spinalcordtoolbox/process_seg.py#L50 The shape metrics are then outputted into...

Update/replace [NeuroLibre preprint refs](https://neurolibre.org/papers/10.55458/neurolibre.00017) by [peer-reviewed Imaging Neuroscience ref](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00075/119044/A-database-of-the-healthy-human-spinal-cord): https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/29476b99e05d59a2b42ed7d20d4f40a58a53c497/spinalcordtoolbox/scripts/sct_process_segmentation.py#L93-L96 https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/29476b99e05d59a2b42ed7d20d4f40a58a53c497/spinalcordtoolbox/scripts/sct_compute_compression.py#L60-L62

List of `sct_qc` commands that reuse existing QC layouts for new applications

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## Background The `sct_qc` command allows users to generate QC reports in a flexible way, compared to running scripts with the `-qc` option. To select a QC report, we use...

Include `manual-correction` repo to SCT tutorial

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Update [spinalcordtoolbox.com _What if things go wrong?_ section](https://spinalcordtoolbox.com/user_section/tutorials/analysis-pipelines-with-sct/handling-issues.html) with [manual-correction](https://github.com/spinalcordtoolbox/manual-correction) repo. Related: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4186

`sct_compute_compression` fails when processing several subjects in parallel

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When running `sct_compute_compression -normalize-hc 1 -o compression_metrics.csv` (see lines [here](https://github.com/sct-pipeline/dcm-metric-normalization/blob/d985ac0ca24d6253bfe717310f4c6a3529243b60/scripts/process_data_dcm-zurich.sh#L198-L206)) across multiple-subjects at once using the `sct_run_batch -jobs 32` wrapper on a cluster, the `sct_compute_compression` fails for some subjects. Namely...

Output images have their unused `dim`/`pixdim` values overwritten with `1.0`

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### Description When running: ``` sct_deepseg_sc -i sub-001_T1w.nii.gz -c t1 ``` The output SC seg has a different `pixdim` that the input image: ``` $ sct_image -i sub-001_T1w.nii.gz -header |...