What if things go wrong?

If you spot any issues during QC, e.g., error during segmentation, you can correct the issue (manually or by adjusting SCT parameters), and then re-run the processing.

process_data.sh contains a number of convenience functions that will select any file with suffix -manual, if it exists, then use that file (instead of automatically computing, e.g., a segmentation). That way, you can manually process outlier subjects without interrupting the automated processing for the dataset as a whole.