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This issue summarizes experiments related to `Dataset601_DCMlesions` (region-based model trained to using a single input channel (T2w_ax) to segment both SC and lesions).
`dataset.json`:
```json…
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# Description
## Data
- `nih-ms-mp2rage`
- `marseille-7T-iso-mp2rage`
- `marseille-7T-aniso-mp2rage`
As discussed [here](https://github.com/ivadomed/model_seg_ms_mp2rage/issues/75#issuec…
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# Description
It has been observed that manual segmentations of SC in MP2RAGE datas (`basel-mp2rage` `marseille-3T-mp2rage`) have some issues like:
- #266
- SC masks does not cover the entire…
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## Context
The Montreal team would like to share spinal cord lesion segmentation obtained by @plbenveniste to the Toronto team (@leelisae) for the purpose of linking spinal cord lesion load with ad…
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Some POs such as PLANP and MP represent lesions. PLANP in particular needs to represent lesions and their very particular shape. In MP, some lesions are represented as process phenotypes (example:[ sk…
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Segmentation algorithms are often confused by lesioned areas, resulting in incorrect automated segmentation results in these regions. As such, it is good practice is to subtract the lesion mask from t…
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There was some confusion about how and when to use [`manual_correction.py`](https://github.com/spinalcordtoolbox/manual-correction/blob/main/manual_correction.py) script. This issue intends to clarify…
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### Description
We want to update SPM12 and CAT12 to a more recent version; it probably makes sense to update both at the same time given their interdependence, and carefully test several scenarios…
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- [x] Explore and understand the CanProCo dataset then select the data to use for training
- [x] Data-preprocessing for nnU-Net format
- [x] Code orientation correction script
- [x] Train a 3D nnU-…
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## Description
The objective would be to generate susceptibility maps of the spine and the brain using segmentations generated for the dataset `whole-spine`.
## Current state
Currently, segme…