diff --git a/derivatives/labels_softseg/README.txt b/derivatives/labels_softseg/README.txt index e37728ba0c..71f8f44936 100644 --- a/derivatives/labels_softseg/README.txt +++ b/derivatives/labels_softseg/README.txt @@ -1,18 +1,11 @@ -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) diff --git a/derivatives/labels_softseg_bin/README.md b/derivatives/labels_softseg_bin/README.md new file mode 100644 index 0000000000..dc82ec3a2a --- /dev/null +++ b/derivatives/labels_softseg_bin/README.md @@ -0,0 +1,5 @@ +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)