zeigar / oxford_asl

A command line tool for quantification of perfusion from ASL data

OXFORD_ASL

A command line tool for quantification of perfusion from ASL data

oxford_asl is part of the BASIL toolbox within FSL for the analysis of perfusion ASL data. oxford_asl provides a single means to quantify CBF from ASL data, including kinetic-model inversion, absolute quantification via a calibration image and registration of the data. It provides most of the common options that someone who has raw ASL data might like to perform to extract perfusion images and thus is the normal place to begin for most users who want a command line tool.

oxford_asl is the main underlying tool behind the equivalent graphical user interface: Asl_gui. To use oxford_asl you may find you first need to pre-process your data using asl_file (see the tutorial for examples where this is relevant). More advanced users wishing to do customised kinetic analysis might want to use the basil command line tool - this is the very core of oxford_asl and thus the BASIL toolbox overall.

Referencing

If you use oxford_asl 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 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.24372