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.
The tools are meant to be integrated into a workflow manager: https://github.com/UoMResearchIT/radnet_core_pipelines/
Developed in the framework of the RADNET project.
madym_T1.cwl: T1 mapping from Inversion Recovery (IR) or Variable Flip Angle (VFA) datamadym_DCE.cwl: fits tracer-kinetic models to Dynamic Contrast Enhanced (DCE) time-seriesDCE_deltaCt.cwl: calculates change in contrast agent concentration C(t) from DCE time-seriesOE_deltaR1.cwl: calculates change in R1 relaxation rate from Oxygen Enhanced (OE) time-seriesOE_DCE_summary.cwl[PENDING!]: apply ROI masks to DCE and OE data and calculate summary statistics
OE_IR:madym_T1 (IR_E)+OE_deltaR1DCE_VFA:madym_T1 (VFA)+OE_deltaCt+madym_DCE (ETM)OE_IR_DCE_VFA:OE_IR+DCE_VFA+ [PENDING!]OE_DCE_summary
There's an example input file for each tool/workflow in the test directory.
Relative file paths ares set to work with data placed under test/data.
The script load_test_data.sh will to place symlinks to the required subdirectories (dce, oe, IR, VFA) in the right place:
bash test/load_test_data.sh <DATA_DIR> [<sub-directories>]If the data does not conform to this structure, the input files will need to be edited accordingly. Relative paths are interpreted as relative to the input file's location.
The script run_tests.sh will attempt to run (all) tests on the linked data, generating output in test/output. To test a given tool or workflow, use the -t option, e.g.:
bash test/run_tests.sh -t OE_IR_DCE_VFAThis is equivalent to the cwltool command:
# cd ./test
cwltool --outdir output/workflows/OE_IR_DCE_VFA --cachedir cache/OE_IR_DCE_VFA \
../workflows/OE_IR_DCE_VFA.cwl workflows/OE_IR_DCE_VFA_test.yml > output/OE_IR_DCE_VFA.cwl.log 2>&1TODO: generate synthetic data and automate tests