pipeline_qc.pl
generate QC images for T1/mask and T1/T2 overlays
pipeline_qc.pl <mask> <t1> <t2> <candID> <visit> <age> <out_t1msk.jpg> <out_t1t2.jpg>
DESCRIPTION
pipeline_qc.pl generates quality control (QC) images for visual inspection of processing results. It produces two output images: a T1-weighted volume with brain mask overlay showing the quality of brain extraction, and a T1/T2 co-registration overlay showing the alignment between modalities.
The images are annotated with the candidate ID, visit label, and age for easy identification during QC review. The –fake option generates placeholder images without performing actual rendering, useful for pipeline testing.
OPTIONS
--verbose- Print progress information during processing.
--fake- Generate placeholder QC images without performing actual rendering. Useful for testing pipeline flow.
--clobber- Overwrite output files if they already exist.
EXAMPLES
Generate QC images for a subject:
pipeline_qc.pl brain_mask.mnc t1_tal.mnc t2_tal.mnc \
CAND001 V1 25 qc_t1mask.jpg qc_t1t2.jpg
Generate with verbose output:
pipeline_qc.pl brain_mask.mnc t1_tal.mnc t2_tal.mnc \
CAND001 V1 25 qc_t1mask.jpg qc_t1t2.jpg --verbose
Generate placeholder images for testing:
pipeline_qc.pl brain_mask.mnc t1_tal.mnc t2_tal.mnc \
CAND001 V1 25 qc_t1mask.jpg qc_t1t2.jpg --fake
AUTHOR
Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.