Modules

PyASL modules can be freely composed in YAML to build custom preprocessing and quantification workflows. Every module exposes a single entrypoint:

• run(data_descrip: dict, config: dict) (or params)

• data_descrip follows ASL-BIDS semantics (e.g., Images, ASLContext, M0Type)

• config/params are taken from your YAML

Note

PyASL mirrors rawdata to derivatives. Most modules automatically read from paths under rawdata and write to the corresponding derivatives/<sub>/<modality> locations.

• Coregister (SPM / ASLtbx)
  • Inputs & prerequisites
  • Outputs & filenames
  • Configuration (YAML → config)
  • YAML example
• Realign (SPM)
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• Smooth (SPM)
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• ResetOrientation
  • What it touches
  • Outputs
  • Configuration
  • YAML example
• CreateMask
  • Inputs
  • Outputs & filenames
  • Configuration
  • YAML example
• PerfusionQuantify (ASLtbx-style)
  • What it does
  • Inputs
  • Outputs & filenames
  • Configuration
  • YAML example
• DLASLBuildMask
  • Inputs & discovery
  • Outputs
  • Configuration
  • YAML example
• DLASLDenoiseCBF
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudReadMPR
  • Behavior
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudRescale
  • Behavior
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudCalculateDiffmap
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudCalculateM0
  • What it does
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudCalculateCBF
  • Workflow
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudMultidelayCalculateM0
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudMultidelayCalculateCBFATT
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudCoregMPR
  • Workflow
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• MRICloudT1ROICBFAverage
  • Inputs
  • Outputs
  • ROI levels & mapping
  • Configuration
  • YAML example
• OxfordASLRun
  • What it builds
  • Inputs
  • Outputs
  • Configuration (params)
  • YAML example
• OxfordASLSplitM0
  • Inputs
  • Outputs
  • Configuration
  • YAML example
• NIfTILoader (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• BrukerLoader (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• ControlLabelSplit (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• SteadyStateTrim (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• DiffImage (Preclinical)
  • Context I/O
  • YAML example
• ComputeM0 (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• CBFRelative (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• BrainMask (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• SlicePLDAdjust (Preclinical)
  • Context I/O
  • Parameters
  • YAML example
• AbsCBF_T1Fit (Preclinical)
  • Computation
  • Context I/O
  • Filesystem outputs
  • Parameters
  • YAML example
• MotionCheck (Preclinical)
  • Context I/O
  • YAML example
• SaveOutputs (Preclinical)
  • Context I/O
  • Parameters
  • YAML example