BASIL toolset

BASIL is a collection of tools that aid in the creation of quantitative CBF images from ASL data. It is available within FSL (v6.0.1 or later is strongly recommended).

BASIL includes complete high-level pipelines for processing ASL data and also individual tools for more bespoke analysis.

• ASL Analysis Guide
  • Perfusion Quantification using Arterial Spin Labelling MRI
• Overview of the BASIL toolset
  • Higher-level packages
  • Individual analysis tools
• Tutorials
  • Worked examples from the FSL course
  • Cerebrovascular Reserve Quantification Using ASL
  • Command line Tutorial
  • Preparatory materials
• GUI User Guide
  • Input Data
  • Structural
  • Calibration
  • Distortion Correction
  • Analysis
  • Output
• Command line User Guide
  • Overview
  • What you will need
  • Things to note
  • Typical Usage
  • Output
  • Detailed usage information
  • Region analysis
• Other components of the BASIL toolset
  • BASIL (command)
  • asl_calib - calibration of ASL perfusion
  • asl_file - preprocessing of ASL data
  • QUASIL - quantification of QUASAR data
  • TOAST - quantification of Turbo-QUASAR data

References

If you employ BASIL in your research please reference the article below, plus any others that specifically relate to the analysis you have performed:

• Michael A. Chappell, Thomas F. Kirk, Martin S. Craig, Flora A. Kennedy McConnell, Moss Y. Zhao, Bradley J. MacIntosh, Thomas W. Okell, Mark W. Woolrich; BASIL: A toolbox for perfusion quantification using arterial spin labelling. Imaging Neuroscience 2023; 1 1–16. doi: https://doi.org/10.1162/imag_a_00041

For detail of the Variational Bayes method employed in Basil:

• Chappell MA, Groves AR, Whitcher B, Woolrich MW. Variational Bayesian inference for a non-linear forward model. IEEE Transactions on Signal Processing 57(1):223-236, 2009.

If you employ spatial regularisation (priors) you should ideally reference this article too:

• A.R. Groves, M.A. Chappell, M.W. Woolrich, Combined Spatial and Non-Spatial Prior for Inference on MRI Time-Series , NeuroImage 45(3) 795-809, 2009.

If you fit the macrovascular (arterial) contribution you should reference this article too.

• Chappell MA, MacIntosh BJ, Donahue MJ, Gunther M, Jezzard P, Woolrich MW. Separation of Intravascular Signal in Multi-Inversion Time Arterial Spin Labelling MRI. Magn Reson Med 63(5):1357-1365, 2010.

If you employ the partial volume correction method then you should reference this article too.

• Chappell MA, MacIntosh BJ, Donahue MJ,Jezzard P, Woolrich MW. Partial volume correction of multiple inversion time arterial spin labeling MRI data, Magn Reson Med, 65(4):1173-1183, 2011.

If you perform model-based analysis of QUASAR ASL data then you should reference this article too.

• Chappell, M. A., Woolrich, M. W., Petersen, E. T., Golay, X., & Payne, S. J. (2012). Comparing model-based and model-free analysis methods for QUASAR arterial spin labeling perfusion quantification. doi:10.1002/mrm.243