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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). | ||
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Main processing steps include: | ||
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- 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 | ||
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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) |
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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. | ||
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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) |