Nathan Molinier

## Description I'm trying to run total segmentator MRI but run into an error: ``` If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024 Traceback (most recent call last): File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/bin/TotalSegmentator",...

Adding a new `nnUNetTrainer` variant for extensive data augmentations

5

Hello nnUNet Community, I'm working on segmenting various anatomical structures from MRI scans. A major challenge in training models on MRI scans is ensuring they generalize across different MRI contrasts...

Improve `sct_qc` usage for totalspineseg

1

## Description QCing totalspineseg segmentation with `-p sct_label_vertebrae` is limited, because this was not designed to deal with segmentations. Moreover, other features should be added to ease the quality control....

Allow the use of custom mapping for `sct_label_vertebrae`

1

## Checklist - [x] **PR Sidebar**: I've filled in each of the options within the PR sidebar. ([Reviewers](https://github.com/spinalcordtoolbox/spinalcordtoolbox/wiki/Contributing:-Submitting-changes-to-SCT-(Opening-a-Pull-Request)#231-reviewers), [Assignees](https://github.com/spinalcordtoolbox/spinalcordtoolbox/wiki/Contributing:-Submitting-changes-to-SCT-(Opening-a-Pull-Request)#232-assignees), [Labels](https://github.com/spinalcordtoolbox/spinalcordtoolbox/wiki/Contributing:-Submitting-changes-to-SCT-(Opening-a-Pull-Request)#233-labels) (**exactly one** dark purple label!), [Milestone](https://github.com/spinalcordtoolbox/spinalcordtoolbox/wiki/Contributing:-Submitting-changes-to-SCT-(Opening-a-Pull-Request)#234-milestone), [Development](https://github.com/spinalcordtoolbox/spinalcordtoolbox/wiki/Contributing:-Submitting-changes-to-SCT-(Opening-a-Pull-Request)#235-development).) - [ ]...

Rename `sct_deepseg totalspineseg` output to make it more user friendly

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## Description Using `totalspineseg` through `sct_deepseg` may not be entirely user-friendly, particularly because the current naming conventions—such as `step1` and `step2` can be unclear for users unfamiliar with the [main...

Adding a new `nnUNetTrainer` variant for extensive data augmentations on `GPU`

5

## Description Hello nnUNet Community, I am currently working on a project exploring how data augmentations can improve model performance for 3D segmentation tasks on MRI images, using nnUNet as...