We are excited to announce a new major and historic release of Diffusion Imaging in Python (DIPY). DIPY 1.0.0 is out! Please cite using the following DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385> DIPY 1.0.0 (Monday, 5 August 2019) This release received contributions from 17 developers (the full release notes are at: https://dipy.org/documentation/1.0.0./release_notes/release1.0/). Thank you all for your contributions and feedback! A new DIPY era is starting: this release is compatible with python 3.5+ and breaks backward compatibility with 0.x.x. Please click here <https://dipy.org/documentation/1.0.0./api_changes/> to check API changes or look at the end of this email. The 0.16.x series will have extended bug-fix-only support for Python 2.7 until June 2020. Highlights of this release include: - Critical API changes <https://dipy.org/documentation/1.0.0./api_changes/> - New awesome website <http://dipy.org> - Large refactoring of tracking API - New denoising algorithm: MP-PCA - New Gibbs ringing removal - New interpolation module: dipy.core.interpolation - New reconstruction models: Mean Signal DKI, MTMS-CSD - 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 Note: - DIPY 0.16.x will be the last series to support python 2. The next release, DIPY 1.0, will support python 3 only. To upgrade or install <http://dipy.org/release0.10.html> DIPY Run the following command in your terminal: <http://dipy.org/release0.10.html> pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (2.4.0+). For visualization you need FURY (0.3.0+). Questions or suggestions? For any questions go to http://dipy.org, or send an e-mail to dipy@python.org <neuroimaging@python.org> We also have an instant messaging service and chat room available at https://gitter.im/nipy/dipy On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors API Changes Some of the changes introduced in the 1.0 release will break backwards compatibility with previous versions. This release is compatible with Python 3.5+ Reconstruction The spherical harmonics bases mrtrix and fibernav have been renamed to tournier07 and descoteaux07 after the deprecation cycle started in the 0.15 release. We changed dipy.data.default_sphere from symmetric724 to repulsion724 which is more evenly distributed. Segmentation The API of dipy.segment.mask.median_otsu has changed in the following ways: if you are providing a 4D volume, vol_idx is now a required argument. The order of parameters has also changed. Tractogram loading and saving The API of dipy.io.streamlines.load_tractogram and dipy.io.streamlines.save_tractogram has changed in the following ways: When loading trk, tck, vtk, fib, or dpy) a reference nifti file is needed to guarantee proper spatial transformation handling. Spatial transformation handling Functions from dipy.tracking.streamlines were modified to enforce the affine parameter and uniform docstrings. deform_streamlines select_by_rois, orient_by_rois, _extract_vals and values_from_volume. Functions from dipy.tracking.utils were modified to enforce the affine parameter and uniform docstring. density_map connectivity_matrix, seeds_from_mask, random_seeds_from_mask, target, target_line_based, near_roi, length and path_length were all modified. The function affine_for_trackvis, move_streamlines, flexi_tvis_affine and get_flexi_tvis_affine were deleted. Functions from dipy.tracking.life were modified to enforce the affine parameter and uniform docstring. voxel2streamline, setup and fit from class FiberModel were all modified. afq_profile from dipy.stats.analysis was modified in a similar way. Simulations - dipy.sims.voxel.SingleTensor has been replaced by dipy.sims.voxel.single_tensor - dipy.sims.voxel.MultiTensor has been replaced by dipy.sims.voxel.multi_tensor - dipy.sims.voxel.SticksAndBall has been replaced by dipy.sims.voxel.sticks_and_ball Interpolation All interpolation functions have been moved to a new module name dipy.core.interpolation Tracking The voxel_size parameter has been removed from the following function: - dipy.tracking.utils.connectivity_matrix - dipy.tracking.utils.density_map - dipy.tracking.utils.stremline_mapping - dipy.tracking._util._mapping_to_voxel The dipy.reconst.peak_direction_getter.PeaksAndMetricsDirectionGetter has been renamed dipy.reconst.peak_direction_getter.EuDXDirectionGetter. The LocalTracking and ParticleFilteringTracking functions were moved from dipy.tracking.local.localtrackingto dipy.tracking.local_tracking. They now need to be imported from dipy.tracking.local_tracking. - functions argument tissue_classifier were renamed stopping_criterion The TissueClassifier were renamed StoppingCriterion and moved from dipy.tracking.local.tissue_classifier to dipy.tracking.stopping_criterion. They now need to be imported from dipy.tracking.stopping_criterion. - TissueClassifier -> StoppingCriterion - BinaryTissueClassifier -> BinaryStoppingCriterion - ThresholdTissueClassifier -> ThresholdStoppingCriterion - ConstrainedTissueClassifier -> AnatomicalStoppingCriterion - ActTissueClassifier -> ActStoppingCriterion - CmcTissueClassifier -> CmcStoppingCriterion The dipy.tracking.local.tissue_classifier.TissueClass was renamed dipy.tracking.stopping_criterion.StreamlineStatus. The EuDX tracking function has been removed. EuDX tractography can be performed using dipy.tracking.local_tracking using dipy.reconst.peak_direction_getter.EuDXDirectionGetter. Streamlines dipy.io.trackvis has been removed. Use dipy.io.streamline instead. Other - dipy.external package has been removed. - dipy.fixes package has been removed. - dipy.segment.quickbundes module has been removed. - dipy.reconst.peaks module has been removed. - Compatibility with Python 2.7 has been removed