Published March 8, 2017 | Version v1.0.8b
Software Open

preprocessed-connectomes-project/quality-assessment-protocol: QAP v1.0.8

Creators

  • 1. Child Mind Institute
  • 2. Stanford University
  • 3. Columbia University Libraries @cul
  • 4. Nathan S Kline Institute for Pscyhiatric Research and Child Mind Institute
  • 5. Yale University

Description

  • QAP measure outputs and NIFTI header information is now stored in individual participant-level output JSON files instead of single-participant CSVs. At the end of the pipeline run, the information in these JSON files can be consolidated using the qap_jsons_to_csv.py script.
  • Visualization graphs & reports are now generated using the qap_jsons_to_csv.py script upon completion of the pipeline run.
  • Consolidated the data configuration file (participant list) generator scripts into one multi-purpose script (qap_sublist_generator.py), which supports BIDS directory format and AWS S3 bucket file path links.
  • The pipeline configuration YAML file parameter names have been updated to be clearer.
  • Introduction of the qap_check_output_csv.py script, which quickly compares the output CSV file against your original data configuration YAML file, then lists which participant-session-scans are missing in the final output and creates a new data configuration file with these scans for a convenient re-run.
  • Users can now select to have zeros removed from anatomical scans prior to processing via the pipeline configuration file with the "exclude_zeros" flag. This is useful if a large number of zeros have been introduced to anatomical scans during de-facing and de-earing of images for privacy compliance, which can skew the QAP metric results.
  • Improved information & error reporting.
  • Fixed a bug where not all participants listed in the data configuration file would be run.
  • Fixed several bugs that were causing report/PDF generation to crash or fail to complete.

Files

preprocessed-connectomes-project/quality-assessment-protocol-v1.0.8b.zip

Files (42.1 MB)

Additional details

Related works

Is supplement to
https://github.com/preprocessed-connectomes-project/quality-assessment-protocol/tree/v1.0.8b (URL)