Nathan Molinier

## Description Right now, it is not possible to quality control (QC) segmentations using the sagittal view when the spinal cord (SC) mask is not specified. From my understanding of...

Training dataset identification for sct deep learning based methods

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### Backgroung SCT provides several functions based on deep learning methods : `sct_deepseg_sc`.. The performances of these methods mainly depend on the quality and the quantity of the data used...

Sagittal mosaic QC report is tiny for 1.0mm istropic image with 75 slices

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## Description I was experimenting with QC generation on spine segmentation and figured that I could use the flag `-p sct_deepseg_lesion` to quality control my data. Example ```python subprocess.check_call([ "sct_qc",...

SCT uses the reverse convention for orientation strings compared to nibabel/BIDS/FSL: 'RPI' (-) vs. 'LAS' (+)

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### Description I did not find any similar issues related to this topic but I would like to understand why we decided not to follow nibabel's orientation convention ? See...

Labels with missing suffixes

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## Description I noticed that for some subjects masks, suffixes are missing: - derivatives/labels_softseg/sub-brnoCeitec01/anat/sub-brnoCeitec01_T1w.nii.gz - derivatives/labels_softseg/sub-barcelona02/anat/sub-barcelona02_flip-1_mt-on_MTS.nii.gz - derivatives/labels_softseg/sub-barcelona02/anat/sub-barcelona02_T2w.nii.gz - derivatives/labels_softseg/sub-balgrist02/anat/sub-balgrist02_flip-1_mt-on_MTS.nii.gz @sandrinebedard should we just add `_softseg` ?

## Description In this [issue](https://github.com/spinalcordtoolbox/disc-labeling-hourglass/issues/6) a comment was made by @jcohenadad and @sandrinebedard to potentially correct some C1 labels. ## Example In the previous issue, the case of the patient...

## Description This PR update JSON sidecars according to our new convention. Only 1766/3148 json in the folder `derivatives/labels` will be modified by this PR. The remaining json in the...

## Description > ⚠️ This PR only affects the derivative folder `label` as well as some raw images This PR fixes: - miss usage of the BIDS entity `space-other` -...

Add spine discrete segmentation and canal segmentation from totalspineseg project

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## Description This PR adds spine discrete segmentations and canal segmentations to the dataset. These segmentations were generated for almost all the subject during the [totalspineseg](https://github.com/neuropoly/totalspineseg) project and were added...

`sct_register_multimodal` is changing the data type when using nearest neighbours interpolation

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## Description I needed to use `sct_register_multimodal -identity 1 -x nn` to put segmentation masks in the same orientation/space as my images and I noticed that the function was changing...