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South Edinburgh Perfusion+ Analysis Library (SEPAL)

Please note: This library is also hosted in the OSIPI DCE-DSC-MRI_CodeCollection repository, where unit tests and perfusion code by other authors can also be found.

Python library for simulating and fitting DCE- and other quantitative MRI data. It permits arbitrary combinations of pulse sequence, pharmacokinetic model, water exchange model, etc. The code is a work-in-progress, has not been extensively tested and is not recommended or approved for clinical use.

Created 28 September 2020
@authors: Michael Thrippleton
@email: m.j.thrippleton@ed.ac.uk
@institution: University of Edinburgh, UK

Installation:

pip install sepal

Use:

Most functionality is demonstrated in Jupyter notebook format in ./demo

Functionality:

  • Enhancement-to-concentration conversion (assuming fast water exchange)
  • Fit tissue concentration using pharmacokinetic model
  • Fit signal enhancement using pharmacokinetic model
  • Pharmacokinetic models: steady-state, Patlak, extended Tofts, Tofts, 2CXM, 2CUM
  • Patlak fitting with multiple linear regression
  • AIFs: including patient-specific (measured), Parker, bi-exponential Parker
  • Fitting free AIF time delay parameter
  • Relaxivity models: linear
  • Signal models: spoiled gradient echo, inversion-recovery spin-echo
  • Water exchange models: FXL, NXL, NXL_be
  • T1 fitting using variable flip angle method, IR-SPGR, DESPOT1-HIFI and inversion recovery
  • T2(*) fitting for multi-TE acquisitions
  • MTR and MTSat calculation

Not yet implemented/limitations:

  • Additional pharmacokinetic models (add by inheriting from PkModel class)
  • Additional relaxivity models (add by inheriting from CRModel class)
  • Additional water exchange models, e.g. 3S2X, 2S1X (add by inheriting from WaterExModel class)
  • Additional signal models (add by inheriting from SignalModel class)
  • R2/R2* effects not included in fitting of enhancement curves (but is included for enhancement-to-concentration conversion)
  • Compartment-specific relaxivity parameters/models
  • Fitting water exchange parameters

Updates

Release 1.1.1 - roi_measure exclude NaNs when calculating percentiles Release 1.1.0 - roi_measure modified to generate more ROI statistics Release 1.0.3 - Add exception handling for some zero/negative inputs.
Release 1.0.2 - Changed AIF interpolation method to linear to further reduce oscillations.
Release 1.0.1 - Changed AIF interpolation method to avoid oscillations. Added demo notebook on interpolation.