Dipy is a diffusion MR imaging library written in Python
'Close gh-' statements refer to GitHub issues that are available at:
http://github.com/dipy/dipy/issues
The full VCS changelog is available here:
http://github.com/dipy/dipy/commits/master
The code found in Dipy was created by the people found in the AUTHOR file.
- 1.9.0 (Friday, March 8, 2023)
- Numpy 2.0.0 support.
- DeepN4 novel DL-based N4 Bias Correction method added.
- Multiple Workflows added.
- Large update of DIPY Horizon features.
- Pytest for Cython files(*.pyx) added.
- Large documentation update.
- Support of Python 3.8 removed.
- Closed 139 issues and merged 58 pull requests.
- 1.8.0 (Wednesday, December 13, 2023)
- Python 3.12.0 support.
- Cython 3.0.0 compatibility.
- Migrated to Meson build system. Setuptools is no more.
- EVAC+ novel DL-based brain extraction method added.
- Parallel Transport Tractography (PTT) 10X faster.
- Many Horizon updates. Fast overlays of many images.
- New Correlation Tensor Imaging (CTI) method added.
- Improved warnings for optional dependencies.
- Large documentation update. New theme/design integration.
- Closed 197 issues and merged 130 pull requests.
- 1.7.0 (Sunday, April 23, 2023)
- NF: BundleWarp - Streamline-based nonlinear registration method for bundles added.
- NF: DKI+ - Diffusion Kurtosis modeling with advanced constraints added.
- NF: Synb0 - Synthetic b0 creation added using deep learning added.
- NF: New Parallel Transport Tractography (PTT) added.
- NF: Fast Streamline Search algorithm added.
- NF: New denoising methods based on 1D CNN added.
- Handle Asymmetric Spherical Functions.
- Large update of DIPY Horizon features.
- Multiple Workflows updated
- Large codebase cleaning.
- Large documentation update. Integration of Sphinx-Gallery.
- Closed 53 issues and merged 34 pull requests.
- 1.6.0 (Monday, January 16, 2023)
- NF: Unbiased groupwise linear bundle registration added.
- NF: MAP+ constraints added.
- Generalized PCA to less than 3 spatial dims.
- Add positivity constraints to QTI.
- Ability to apply Symmetric Diffeomorphic Registration to points/streamlines.
- New Human Connectome Project (HCP) data fetcher added.
- New Healthy Brain Network (HBN) data fetcher added.
- Multiple Workflows updated (DTIFlow, LPCAFlow, MPPCA) and added (RUMBAFlow).
- Ability to handle VTP files.
- Large codebase cleaning.
- Large documentation update.
- Closed 75 issues and merged 41 pull requests.
- 1.5.0 (Friday, March 11, 2022)
- New reconstruction model added: Q-space Trajectory Imaging (QTI).
- New reconstruction model added: Robust and Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD).
- New reconstruction model added: Residual block Deep Neural Network (ResDNN).
- Masking management in Affine Registration added.
- Multiple Workflows updated (DTIFlow, DKIFlow, ImageRegistrationFlow) and added (MotionCorrectionFlow).
- Compatibility with Python 3.10 added.
- Migrations from Azure Pipeline to Github Actions.
- Large codebase cleaning.
- New parallelisation module added.
dipy.io.bvectxt
module deprecated.- New DIPY Horizon features (ROI Visualizer, random colors flag).
- Large documentation update.
- Closed 129 issues and merged 72 pull requests.
- 1.4.1 (Thursday, May 6, 2021)
- Patch2Self and its documentation updated.
- BUAN and Recobundles documentation updated.
- Standardization and improvement of the multiprocessing / multithreading rules.
- Community and governance information added.
- New surface seeding module for tractography named mesh.
- Large update of Cython code in respect of the last standard.
- Large documentation update.
- Closed 61 issues and merged 28 pull requests.
- 1.4.0 (Tuesday, March 14, 2021)
- New self-supervised denoising algorithm Patch2Self added.
- BUAN and RecoBundles documentation updated.
- Response function refactored and clarified.
- B-tensor allowed with response functions.
- Large Command Line Interface (CLI) documentation updated.
- Public API for Registration added.
- Large documentation update.
- Closed 47 issues and merged 19 pull requests.
- 1.3.0 (Tuesday, November 3, 2020)
- Gibbs ringing correction 10X faster.
- Spherical harmonics basis definitions updated.
- Added SMT2 metrics from mean signal diffusion kurtosis.
- New interface functions added to the registration module.
- New linear transform added to the registration module.
- New tutorials for DIPY command line interfaces.
- Fixed compatibility issues with different dependencies.
- Tqdm (multiplatform progress bar for data downloading) dependency added.
- Large documentation update.
- Bundle section highlight from BUAN added in Horizon.
- Closed 134 issues and merged 49 pull requests.
- 1.2.0 (Tuesday, September 9, 2020)
- New command line interfaces for group analysis: BUAN.
- Added b-tensor encoding for gradient table.
- Better support for single shell or multi-shell response functions.
- Stats module refactored.
- Numpy minimum version is 1.2.0.
- Fixed compatibilities with FURY 0.6+, VTK9+, CVXPY 1.1+.
- Added multiple tutorials for DIPY command line interfaces.
- Updated SH basis convention.
- Improved performance of tissue classification.
- Fixed a memory overlap bug (multi_median).
- Large documentation update (typography / references).
- Closed 256 issues and merged 94 pull requests.
- 1.1.1 (Friday, January 10, 2020)
- New module for deep learning
dipy.nn
(uses TensorFlow 2.0). - Improved DKI performance and increased utilities.
- Non-linear and RESTORE fits from DTI compatible now with DKI.
- Numerical solutions for estimating axial, radial and mean kurtosis.
- Added Kurtosis Fractional Anisotropy by Glenn et al. 2015.
- Added Mean Kurtosis Tensor by Hansen et al. 2013.
- Nibabel minimum version is 3.0.0.
- Azure CI added and Appveyor CI removed.
- New command line interfaces for LPCA, MPPCA and Gibbs unringing.
- New MSMT CSD tutorial added.
- Horizon refactored and updated to support StatefulTractograms.
- Speeded up all cython modules by using a smarter configuration setting.
- All tutorials updated to API changes and 2 new tutorials added.
- Large documentation update.
- Closed 126 issues and merged 50 pull requests.
- 1.0.0 (Monday, 5 August 2019)
- Critical :doc:`API changes <api_changes>`
- Large refactoring of tracking API.
- New denoising algorithm: MP-PCA.
- New Gibbs ringing removal.
- New interpolation module:
dipy.core.interpolation
. - New reconstruction models: MTMS-CSD, Mean Signal DKI.
- Increased coordinate systems consistency.
- New object to manage safely tractography data: StatefulTractogram
- New command line interface for downloading datasets: FetchFlow
- Horizon updated, medical visualization interface powered by QuickBundlesX.
- Removed all deprecated functions and parameters.
- Removed compatibility with Python 2.7.
- Updated minimum dependencies version (Numpy, Scipy).
- All tutorials updated to API changes and 3 new added.
- Large documentation update.
- Closed 289 issues and merged 98 pull requests.
- 0.16.0 (Sunday, 10 March 2019)
- Horizon, medical visualization interface powered by QuickBundlesX.
- New Tractometry tools: Bundle Analysis / Bundle Profiles.
- New reconstruction model: IVIM MIX (Variable Projection).
- New command line interface: Affine and Diffeomorphic Registration.
- New command line interface: Probabilistic, Deterministic and PFT Tracking.
- Integration of Cython Guidelines for developers.
- Replacement of Nose by Pytest.
- Documentation update.
- Closed 103 issues and merged 41 pull requests.
- 0.15 (Wednesday, 12 December 2018)
- 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.
- 0.14 (Tuesday, 1 May 2018)
- RecoBundles: anatomically relevant segmentation of bundles
- New super-fast clustering algorithm: QuickBundlesX
- New tracking algorithm: Particle Filtering Tracking.
- New tracking algorithm: Probabilistic Residual Bootstrap Tracking.
- Integration of the Streamlines API for reading, saving and processing tractograms.
- Fiber ORientation Estimated using Continuous Axially Symmetric Tensors (Forecast).
- New command line interfaces.
- Deprecated fvtk (old visualization framework).
- A range of new visualization improvements.
- Large documentation update.
- 0.13 (Monday, 24 October 2017)
- Faster local PCA implementation.
- Fixed different issues with OpenMP and Windows / OSX.
- Replacement of cvxopt by cvxpy.
- Replacement of Pytables by h5py.
- Updated API to support the latest numpy version (1.14).
- New user interfaces for visualization.
- Large documentation update.
- 0.12 (Tuesday, 26 June 2017)
- 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 the latest numpy versions.
- New system for automatically generating command line interfaces.
- Faster computation of the Cross-Correlation metric for registration.
- 0.11 (Sunday, 21 February 2016)
- New framework for the 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.
- 0.10 (Thursday, 2 December 2015)
- 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.
- New framework for affine registration of images.
- 0.9.2 (Wednesday, 18 March 2015)
- Anatomically Constrained Tissue Classifiers for Tracking
- Massive speedup of Constrained Spherical Deconvolution (CSD)
- Recursive calibration of the response function for CSD
- New experimental framework for clustering
- Improvements and 10X speedup for Quickbundles
- Improvements in Linear Fascicle Evaluation (LiFE)
- New implementation of Geodesic Anisotropy
- New efficient transformation functions for registration
- Sparse Fascicle Model supports acquisitions with multiple b-values
- 0.8.0 (Tuesday, 6 Jan 2015)
- Nonlinear Image-based Registration (SyN)
- Streamline-based Linear Registration (SLR)
- Linear Fascicle Evaluation (LiFE)
- Cross-validation for reconstruction models
- Sparse Fascicle Model (SFM)
- Non-local means denoising (NLMEANS)
- New modular tracking machinery
- Closed 388 issues and merged 155 pull requests
- A variety of bug-fixes and speed improvements
- 0.7.1 (Thursday, 16 Jan 2014)
- Made installing Dipy easier and more universal
- Fixed automated seeding problems for tracking
- Removed default parameter for odf_vertices in EuDX
- 0.7.0 (Monday, 23 Dec 2013)
- Constrained Spherical Deconvolution (CSD)
- Simple Harmonic Oscillator based Reconstruction and Estimation (SHORE)
- Sharpening Deconvolution Transform (SDT)
- Signal-to-noise ratio estimation
- Parallel processing enabled for all reconstruction models using peaks_from_model
- Simultaneous peak and ODF visualization
- Streamtube visualization
- Electrostatic repulsion for sphere generation
- Connectivity matrices and density maps
- Streamline filtering through specific ROIs using target
- Brain extraction and foreground extraction using median_otsu
- RESTORE fitting for DTI
- Westin's Tensor maps
- Access to more publicly available datasets directly through Dipy functions.
- 3x more tutorials than the previous release
- 0.6.0 (Sunday, 24 Mar 2013)
- Cython 0.17+ enforced
- New reconstruction models API
- Diffusion Spectrum Imaging (DSI)
- DSI with deconvolution
- Generalized Q-sampling Imaging 2 (GQI2)
- Modular fiber tracking * deterministic * probabilistic
- Fast volume indexing (a faster ndindex)
- Spherical Harmonic Models * Opdt (Tristan-Vega et. al) * CSA odf (Aganj et. al) * Analytical Q-ball (Descoteaux et. al) * Tuch's Q-ball (Tuch et. al)
- Visualization of spherical functions
- Peak finding in odfs
- Non-linear peak finding
- Sphere Object
- Gradients Object
- 2D sphere plotting
- MultiTensor and Ball & Sticks voxel simulations
- Fetch/Download data for examples
- Software phantom generation
- Angular similarity for comparisons between multiple peaks
- SingleVoxelModel to MultiVoxelModel decorator
- Mrtrix and fibernavigator SH bases
- More Benchmarks
- More Tests
- Color FA and other Tensor metrics added
- Scripts for the ISBI 2013 competition
- Fit_tensor script added
- Radial basis function interpolation on the sphere
- New examples/tutorials
- 0.5.0 (Friday, 11 Feb 2011)
- Initial release.
- Reconstruction algorithms e.g. GQI, DTI
- Tractography generation algorithms e.g. EuDX
- Intelligent downsampling of tracks
- Ultra-fast tractography clustering
- Resampling datasets with anisotropic voxels to isotropic
- Visualizing multiple brains simultaneously
- Finding track correspondence between different brains
- Reading many different file formats e.g. Trackvis or Nifti
- Dealing with huge tractography without memory restrictions
- Playing with datasets interactively without storing
- And much more and even more to come in next releases
- Initial release.