Add flag feature to automatically use all images as primary rather than doing the whole primary T1w dance and pony show

nimh-dsst / dsst-defacing-pipeline

Defacing algorithm to improve and evaluate accuracy for large datasets.

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Add flag feature to automatically use all images as primary rather than doing the whole primary T1w dance and pony show #10

Closed dmoracze closed 1 year ago

dmoracze commented 2 years ago

Provide the user with an option to skip the VisualQC of primary scans before defacing. In other words, run it as a one-shot script that identifies primaries, generates mapping file and runs the defacing commands all with one single command.

Arshitha commented 1 year ago

Visual Inspection of primary scans is now optional. So, the user now only has to run the one script, dsst_defacing_wf.py to deface all the anatomical scans in one shot. The QC failures will have to be dealt in the very end by applying appropriate fixes. The changes have been committed to the integrate-to-bids branch. Will tag the PR once I'm ready.

Arshitha commented 1 year ago

T1 MRI checks is no longer a step in the pipeline.