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 0.15.0 is now available. New features include:

  • Updated RecoBundles for automatic anatomical bundle segmentation.
  • New Reconstruction Model: qtau-dMRI.
  • New command line interfaces (e.g. dipy_slr).
  • New continuous integration with AppVeyor CI.
  • Nibabel Streamlines API now used almost everywhere for better memory management.
  • Compatibility with Python 3.7.
  • Many tutorials added or updated (5 New).
  • Large documentation update.
  • Moved visualization module to a new library: FURY.
  • Closed 287 issues and merged 93 pull requests.

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, you can 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.