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In this issue, I detail the work done:
- to get MS lesion segmentation using the current best model.
- to manually correct those lesion segmentations
I created the file `monai/run_inference.py` …
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Opening this issue thanks to a comment from @leelisae regarding some missing lesion mask at M0.
Related issue #96
On it now with the following config file:
```yaml
FILES_LESION:
- sub-edm1…
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Here is an issue to describe the aggregation of available datasets.
The dataset which are of interest for this project are:
- Labeled datasets
- canproco : PSIR and STIR contrast
- sct-testing…
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In this issue, we describe the work done to manually segment MS lesions in the spinal cord on PSIR and STIR contrasts.
This work is pushed on branch `plb/m12_lesion_seg`
The segmentation predicti…
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The biasfield correction on the FLAIR should be an option to enable or disable, where it is disabled by default. LST may itself try a biasfield correction. In FLAIRs with a large lesion load, biasfiel…
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Opening this issue to discuss the creation of a "Lesion protocol" section.
This paper was mentionned in the discussion : [(Carass et al. 2024)](https://www.sciencedirect.com/science/article/pii/S2…
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Similar to https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3612, this issue is used to keep track of progress on feedback/ideas received from the 2021 SCT Course:
### Planning/organiz…
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Some relevant discussions:
- https://github.com/ivadomed/model_seg_ms_mp2rage/issues/56
- https://github.com/ivadomed/model_seg_ms_mp2rage/issues/13
- https://github.com/ivadomed/canproco/issues/20…
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# Description
139 subjects of the 180 MS subjects in the `basel-mp2rage` database have lesion segmentation pixels (lesion-manualNeuroPoly mask) that are outside the SC segmentation
Here an examp…
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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…