adding preprocessing script

[rohanbanerjee]

This PR adds the preprocessing script to clean the mini-bmpd data for training using ivadomed. The script includes the following steps:

• Resizing the ground truth images on the basis of the segmentations using sct_register_multimodal. This is done since a size mismatch was found in between the gt and the segmentations.
• Removal of the unwanted files generated from sct_register_multimodal and renaming the resized image as per the BIDS convention.

To run the script:

• Get the data

git clone [email protected]:datasets/mni-bmpd

• Run the script using:

sct_run_batch -path-data ./mni-bmpd -path-output ./processed_data -jobs -1 -script preprocess.sh

To be done:

• Add a config.yml file for path folders for better reproducibility