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update readme with release of code
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sandrinebedard committed Apr 3, 2024
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15 changes: 4 additions & 11 deletions derivatives/labels_softseg/README.txt
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The derivatives labels_softseg include soft segmentations (_softseg) of the spinal cord. Softsegs were generated artificially by averaging binary segmentations of multiple contrasts using [process_data.sh](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/v1.1/process_data.sh).
The derivatives labels_softseg include soft segmentations (_softseg) of the spinal cord. Softsegs were generated artificially by averaging binary segmentations of multiple contrasts using [process_data.sh](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/v2.2/processing_spine_generic/process_data.sh).

Main processing steps include:

- Spinal cord segmentation on 6 contrasts
- Spinal cord segmentation on 6 contrasts (T1w, T2w, T2star, flip-1_mt-on_MTS, flip-2_mt-off and rec-average_dwi)
- Aligning the images with T2w
- Averaging of the segmentations according to each FOV
- Bringing back the segmentations to the original space

All problematic registrations were excluded and the pipeline was run again so the softsegs only include good registrations.
7 subjects were excluded:
- sub-brnoUhb02
- sub-brnoUhb03
- sub-brnoUhb07
- sub-brnoUhb08
- sub-mountSinai03
- sub-oxfordFmrib01
- sub-ucdavis07
All problematic registrations or if a contrast was missing were excluded and the pipeline was run again so the softsegs only include good registrations.
Excluded subjects are listed here: [exclude.yml](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/v2.2/exclude.yml)
5 changes: 5 additions & 0 deletions derivatives/labels_softseg_bin/README.md
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The derivatives labels_softseg_bin include binarized soft segmentations (desc-softseg_label-SC_seg) of the spinal cord. Softsegs bin were generated artificially by averaging binary segmentations of multiple contrasts using [process_data.sh](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/v2.2/processing_spine_generic/process_data.sh) followed by binarization.


All problematic registrations or if a contrast was missing were excluded and the pipeline was run again so the softsegs only include good registrations.
Excluded subjects are listed here: [exclude.yml](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/v2.2/exclude.yml)

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