Diffusion Imaging In Python

Dipy is a free and open source software project for computational neuroanatomy, focusing mainly on diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for denoising, registration, reconstruction, tracking, clustering, visualization, and statistical analysis of MRI data.

Highlights

Dipy 0.12.0 is now available. New features include:

  • IVIM Simultaneous modeling of perfusion and diffusion.
  • MAPL, tissue microstructure estimation using Laplacian-regularized MAP-MRI.
  • DKI-based microstructural modelling.
  • Free water diffusion tensor imaging.
  • Denoising using Local PCA.
  • Streamline-based registration (SLR).
  • Fiber to bundle coherence (FBC) measures.
  • Bayesian MRF-based tissue classification.
  • New API for integrated user interfaces.
  • New hdf5 file (.pam5) for saving reconstruction results.
  • Interactive slicing of images, ODFs and peaks.
  • Updated API to support latest numpy versions.
  • New system for automatically generating command line interfaces.
  • Faster computation of cross correlation for image registration.

Dipy 0.11.0 is now available. New features include:

  • New framework for contextual enhancement of ODFs.
  • Compatibility with numpy (1.11).
  • Compatibility with VTK 7.0 which supports Python 3.x.
  • Faster PIESNO for noise estimation.
  • Reorient gradient directions according to motion correction parameters.
  • Supporting Python 3.3+ but not 3.2.
  • Reduced memory usage in DTI.
  • DSI now can use datasets with multiple b0s.
  • Fixed different issues with Windows 64bit and Python 3.5.

Dipy 0.10.1 is now available. New features in this release include:

  • Compatibility with new versions of scipy (0.16) and numpy (1.10).
  • New cleaner visualization API, including compatibility with VTK 6, and functions to create your own interactive visualizations.
  • Diffusion Kurtosis Imaging (DKI): Google Summer of Code work by Rafael Henriques.
  • Mean Apparent Propagator (MAP) MRI for tissue microstructure estimation.
  • Anisotropic Power Maps from spherical harmonic coefficients.
  • A new framework for affine registration of images.

See older highlights.

Announcements

See some of our past announcements

Getting Started

Here is a quick snippet showing how to calculate color FA also known as the DEC map. We use a Tensor model to reconstruct the datasets which are saved in a Nifti file along with the b-values and b-vectors which are saved as text files. Finally, we save our result as a Nifti file

fdwi = 'dwi.nii.gz'
fbval = 'dwi.bval'
fbvec = 'dwi.bvec'

from dipy.io.image import load_nifti, save_nifti
from dipy.io import read_bvals_bvecs
from dipy.core.gradients import gradient_table
from dipy.reconst.dti import TensorModel

data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)

tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data)

save_nifti('colorfa.nii.gz', tenfit.color_fa, affine)

As an exercise try to calculate color FA with your datasets. You will need to replace the filepaths fimg, fbval and fbvec. Here is what a slice should look like.

_images/colorfa.png

Next Steps

You can learn more about how you to use Dipy with your datasets by reading the examples in our Documentation.

Support

We acknowledge support from the following organizations:

  • The department of Intelligent Systems Engineering of Indiana University.
  • The Gordon and Betty Moore Foundation and the Alfred P. Sloan Foundation, through the University of Washington eScience Institute Data Science Environment.
  • Google supported DIPY through the Google Summer of Code Program during Summer 2015 and 2016.