madym_cwl

CWL tool wrappers and workflow templates for QBI-Madym, a C++ toolkit for Quantative MRI analysis developed in the Quantitative Biomedical Imaging Laboratory at the University of Manchester.

Developed in the framework of the RADNET project.

Requirements

• Docker
• CWL runner, e.g. cwltool

Tools

• madym_T1.cwl: T1 mapping from Inversion Recovery (IR) or Variable Flip Angle (VFA) data
• madym_DCE.cwl: fits tracer-kinetic models to Dynamic Contrast Enhanced (DCE) time-series
• DCE_deltaCt.cwl: calculates change in contrast agent concentration C(t) from DCE time-series
• OE_deltaR1.cwl: calculates change in R1 relaxation rate from Oxygen Enhanced (OE) time-series
• OE_DCE_hypoxia_mapping.cwl: Generates hypoxia maps from DCE and OE p-value maps
• OE_DCE_summary.cwl [PENDING!]: apply ROI masks to DCE and OE data and calculate summary statistics

Workflows

• OE_IR: madym_T1 (IR_E) + OE_deltaR1
• DCE_VFA: madym_T1 (VFA) + OE_deltaCt + madym_DCE (ETM)
• OE_IR_DCE_VFA: OE_IR + DCE_VFA + [PENDING!] OE_DCE_summary

Tests

See test/README.md for instructions on running tests.