sct-pipeline / contrast-agnostic-softseg-spinalcord

Contrast-agnostic spinal cord segmentation project with softseg

MIT License

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Merge processing pipelines #22

Closed sandrinebedard closed 2 years ago

sandrinebedard commented 2 years ago

Context

This PR mainly:

Updates README with new processing procedure.
Merges processing of preprocess_data.sh and process_data.sh.
Adds cropping and creation of data_processed_clean in the output folder.

Only the images that have segmentations and soft segmentations are transfered in data_processed_clean.

Procedure to test

Download the spine-generic/data-multi-subject by following the procedure
Go to the branch by running: git checkout sb/121-move-derivatives
Launch processing:

sct_run_batch -jobs -1 -path-data <PATH_DATA> -path-output <PATH-OUTPUT> -script process_data.sh -script-args exclude_reg.yml

An example of the results can be found here: duke:projects/ivadomed/contrast-agnostic-seg/data-multi-subject-test13