Personal tools


QuBIc aims to distribute methods developed in the group as software tools for wider research use.

Our ethos is to try and make the work we do available for other people to try out and use, particularly where we have developed a solution for the analysis of a particular type of data. The reasoning behind this is that we seek to be:

  • Transparent: When it comes to algorithms and analysis methods we try hard to make publications as complete as possible. However, it can still be hard for the reader reproduce the method exactly. By providing our code we want to let others have better access to what we have done, compare it to alternative approaches and improve upon it.
  • Pragmatic: However good our method may be at solving the problem we designed it for there is a barrier to use because it is not trivial to implement. Since we often try to solve problems that are relevant to people who do not have a highly mathematical or engineering background it seems unfair to make the user re-invent the wheel when we already have the code written.
  • Collaborative: Ultimately we want to see research progress and not be held up by making people spend time writing programs that already exist. We are happy to work with people who want to use our methods or even try to improve upon them.

Ultimately it is much more satisfying to develop a new method and see it put to use than simply having a publication, but that being the end of it.

We currently distribute software tools via two main routes: either via Quantiphyse, a graphical user interface to a range of quantitive physiological image analysis methods, and the FMRIB Software Library, which is a library of tools for MR imaging data that is freely distributed for non-comercial research use.

We also share methods directly with collaborators where appropriate. We tend to use this route where the code is still a little less polished or where we are not allowed to put the work up for unrestricted distribution on the internet. If the work falls into this category and you would like to use it (for non-commercial research use) then feel free to contact us, we are generally happy to start new collaborations. Commercial use of our methods/tools are permitted subject to a licensing agreement, which is administered by Oxford University Innovation on behalf of the university.

Tools available through Quantiphyse:

Quantiphyse is available through the OUI Software Store free for academic use.

  • Kinetic modelling for Arterial Spin Labelling MRI
  • Model-based and model-free methods for Chemical Exchange Saturation Transfer
  • Model-based and model-free deconvolution methods for Dynamic Susceptibility Contrast perfusion MRI (contact us to request access).
  • Model-based analysis for Dynamic Contrast Enhanced perfusion MRI (contact us to access preview of new version with more extensive models).
  • Vascular Territory Mapping from Vessel Encoded Arterial Spin Labelling MRI (contact us for this module).
  • Clustering and SLIC based data parcellation/segmentation methods.
  • Motion correction.
  • Full suite of data interrogation, masking and plotting tools.

Tools available through FSL:

  • BASIL - Tools for the quantification of perfusion from Arterial Spin Labelling MRI.
  • FABBER - Tool for the analysis of dual-echo (BOLD and ASL) functional MRI.
  • BayCEST - Tool for the quantitative analysis of Chemical Exchange Saturation Transfer MRI.
  • Verbena - Tool for the quantification of perfusion and haemodynamics from Dynamic Susceptibility Contrast perfusion MRI.

Other work for which we share with collaborators:

  • Matlab tools for the analysis of Vessel Encoded ASL MRI perfusion and angiographic data.
  • Matlab tools for Control Point Interpolation for deconvolution, originally designed for use in perfusion quantification using Dynamic Susceptibility Contrast MRI.
  • Matlab tools for fast Bayesian inference on time series using non-linear models.