Basil

Bayesian Inference for Arterial Spin Labelling MRI

BASIL perfusion image

Arterial Spin Labeling (ASL) MRI is a non-invasive method for the quantification of perfusion. Analysis of ASL data typically requires the inversion of a kinetic model of labeled blood-water inflow along with a separate calculation of the equilibrium magnetization of arterial blood. The BASIL toolbox provides the tools to do this based on Bayeisan inference principles. The toolbox was orginally developed for multi delay (inversion time) data where it can be used to greatest effect, but is also sufficiently fleixble to deal with the widely used single delay form of acquisition.

If you want to perform analysis of a functional experiment with ASL data, i.e. one where you want to use a GLM, then you should consult the perfusion section of FEAT, or if you have dual-echo (combined BOLD and ASL) data then consult FABBER.

For single delay ASL data kinetic model inversion is relatively trivial and solutions to the standard model have been described in the literature. However, there are various advantages to aquiring ASL data at multiple times post-inversion and fitting the resultant data to a kinetic model. This permits problems in perfusion estimation associated with variable bolus arrival time to be avoided, since this becomes a parameter of the model whose value is determined from the data. Commonly the model fitting will be performed with a least squares technique providing parameter estimates, e.g. perfusion and bolus arrival time. In contrast to this BASIL uses a (fast) Bayesian inference method for the model inversion, this provides a number of advantages:

  • Voxel-wise estimation of perfusion and bolus arrival time along with parameter variance (allowing confidence intervals to be calculated).
  • Incorporation of natural varaibility of other model parameters, e.g. values of T1, T1b and labeling/bolus duration.
  • Spatial regularization of the estimated perfusion image.
  • Correction for partial volume effects (where the appropriate segmentation information is available).

While the first two apply specfically to the case of mulitple delay data, the latter are also applicable to single delay ASL and are only available using the Bayesian technique employed by BASIL.

Download

The documentation found here relates to the version of BASIL that can be found in FSL v6.0.1 (and higher). We strongly recommend you use that version in place of the one present in previous FSL releases.

A release of the latest version of the BASIL tools can be found by following the link below. This can be installed alonside an existing FSL 6.0 release.

https://github.com/ibme-qubic/oxford_asl/releases

Examples

An extensive set of examples of the use of BASIL (for pcASL) is availabe as part of the primer:

Introduction to Perfusion Quantification using Arterial Spin Labelling, Oxford Neuroimaging Primers, Chappell, MacIntosh & Okell, Oxford University Press, 2017.

The examples themselves are freely available online at the primer website: neuorimagingprimers.org, you can access the ASL examples directly here.

BASIL tools

BASIL is supplemented by a collection of tools that aid in the creation of quantitative CBF images from ASL data, you should either use one of the higher-level analysis packages or if you want a more specific analysis select the appropriate tool(s) for the data you have.

Higher-level packages

These provide a single means to quantify CBF from ASL data, including kinetic-model inversion, absolute quantification via a calibration image and registration of the data. This will generally be the first place to go for most people who want to do processing of ASL data.

  • asl_gui - The graphical user interface that brings the BASIL tools together in one place.
  • oxford_asl - A command line interface for most common ASL perfusion analysis.

The BASIL toolset

  • BASIL (itself) - this is the core tool that performs kinetic-model inversion to the data using a Bayesian algorithm. You should only need to use it directly for more custom analyses than that offered by oxford_asl/Asl_gui.
  • QUASIL - A special version of BASIL optimised for QUASAR ASL data, includes model-based or model-free analyses along with calibration.
  • asl_calib - this tool takes a supplied calibration volume and calculates the magnetization of arterial blood allowing CBF to be quantified in absolute units. The main functionality of asl_calib is built into oxford_asl, Asl_gui and QUASIL, but more options are available when using it directly.
  • asl_reg - this tool is designed to assist in registration of (low resolution) ASL images to structural or standard brain images. The functionality of asl_reg is built into oxford_asl and Asl_gui.
  • asl_file - a command line tool for the manipulation of ASL data files, particulary designed to cope with the complex strcuture of interleaved lable and control images combined with muliple post-labeling delays.

Further Reading

To learn more about ASL, acquisition choices, the principles of analysis and how perfusion images can be used in group studies you might like to read:

Introduction to Perfusion Quantification using Arterial Spin Labelling, Oxford Neuroimaging Primers, Chappell, MacIntosh & Okell, Oxford University Press, 2017.

Online examples are availble to go with this primer using the BASIL tools. These can be found on the Oxford Neuroimaging Primers website: http://www.neuroimagingprimers.org

The following book reamins a good introduction to functional imaging including perfusion using ASL:

Introduction to Functional Magnetic Resonance Imaging: principles and Techniques. Buxton, Cambridge University Press, 2009.

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:

  • 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