**DIPY 1.9.0** is now available. New features include:

- 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 142 issues and merged 60 pull requests.

====================================
 Release notes for DIPY version 1.9
====================================

GitHub stats for 2023/12/14 - 2024/03/07 (tag: 1.8.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 17 authors contributed 175 commits.

* Ariel Rokem
* Atharva Shah
* Ebrahim Ebrahim
* Eleftherios Garyfallidis
* Gabriel Girard
* John Shen
* Jon Haitz Legarreta Gorroño
* Jong Sung Park
* Maharshi Gor
* Matthew Feickert
* Philippe Karan
* Praitayini Kanakaraj
* Sam Coveney
* Sandro
* Serge Koudoro
* dependabot[bot]
* Étienne Mollier

We closed a total of 139 issues, 60 pull requests and 81 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (60):

* :ghpull:`3095`: [UPCOMING] Release preparation for 1.9.0
* :ghpull:`3086`: [RF] Fix spherical harmonic terminology swap
* :ghpull:`3105`: [doc] improve some tutorials rendering
* :ghpull:`3109`: [BF] convert_tractogram fix
* :ghpull:`3108`: enabled trx support with correct header
* :ghpull:`3107`: enabled trx support for viz
* :ghpull:`3033`: [RF] fix dki mask for nlls
* :ghpull:`3104`: Dkimaskfix
* :ghpull:`3106`: volume slices visibility fixed
* :ghpull:`3102`: Bugfix for peaks slices and synchronization.
* :ghpull:`3078`: return S0 from dki fit
* :ghpull:`3101`: [BF] Uniformize cython version
* :ghpull:`3097`: Feature/surface
* :ghpull:`3048`: [TEST] Adds support of cython for pytest
* :ghpull:`3053`: [NF] Add workflow to convert tensors in different formats
* :ghpull:`3073`: [NF] Add DSI workflow
* :ghpull:`3099`: [DOC] fix some typo [ci skip]
* :ghpull:`3098`: Removing tensorflow addon from DL models
* :ghpull:`2973`: Tab names for slice tabs as file names.
* :ghpull:`3081`: NF: Adding N4 bias correction deep learning model
* :ghpull:`3092`: Feature: volume synchronizing
* :ghpull:`3059`: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors
* :ghpull:`3090`: RF - changed memory view to double* trilinear_interpolation_4d
* :ghpull:`3080`: Adding SH basis legacy option support to peaks_from_model
* :ghpull:`3087`: backward compatibility fixed
* :ghpull:`3088`: [TEST] Pin pytest
* :ghpull:`3084`: fixed 4d slice issue
* :ghpull:`3083`: Np.unique check removed.
* :ghpull:`3082`: Add Fedora installation instructions [ci skip]
* :ghpull:`3076`: [CI] Update scientific-python/upload-nightly-action to 0.5.0
* :ghpull:`3070`: [DOC] Fix installation link in README  [ci skip]
* :ghpull:`3069`: [DOC] Fix DTI Tutorial [ci skip]
* :ghpull:`3063`: [RF] remove cpdef in PmfGen
* :ghpull:`3054`: [DOC] Fix some links [ci skip]
* :ghpull:`3060`: Bump codecov/codecov-action from 3 to 4
* :ghpull:`3061`: [OPT] Enable openmp for macOS wheel and CI's
* :ghpull:`3049`: [MTN] code cleaning: remove some dependencies version checking
* :ghpull:`3050`: [RF] Move ``dipy.boots.resampling`` to  ``dipy.stats.resampling``
* :ghpull:`3051`: [RF] Remove dipy.io.bvectxt module
* :ghpull:`3052`: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874
* :ghpull:`3045`: [DOC] fix `multi_shell_fiber_response` docstring array dims [ci skip]
* :ghpull:`3041`: [NF] Add convert tractograms flow
* :ghpull:`3040`: [BW] Remove some python2 reference
* :ghpull:`3039`: [TEST] Add setup_module and teardown_module
* :ghpull:`3038`: [NF] Update `dipy_info`: allow tractogram files format
* :ghpull:`3043`: d/d/t/test_data.py: endian independent dtype.
* :ghpull:`3042`: pyproject.toml: no cython at run time.
* :ghpull:`3027`: [NF] Add Concatenate tracks workflows
* :ghpull:`3008`: NF: add SH basis conversion between dipy and mrtrix3
* :ghpull:`3025`: [TEST] Manage http errors for stateful tractograms
* :ghpull:`3031`: Bugfix: Horizon image's dtype validation
* :ghpull:`3021`: [MTN] Remove 3.8 Ci's
* :ghpull:`3026`: [RF] Fix cython 3 warnings
* :ghpull:`3022`: [DOC] Fix logo size and link [ci skip]
* :ghpull:`3013`: Added Fibonacci spiral and test for it
* :ghpull:`3019`: DOC: Fix link to toolchain roadmap page in `README`
* :ghpull:`3012`: DOC: Document observance for Scientific Python min supported versions
* :ghpull:`3018`: Bump actions/download-artifact from 3 to 4
* :ghpull:`3017`: Bump actions/upload-artifact from 3 to 4
* :ghpull:`3014`: Update release1.8.rst

Issues (81):

* :ghissue:`2970`: spherical harmonic degree/order terminology swapped
* :ghissue:`3105`: [doc] improve some tutorials rendering
* :ghissue:`3109`: [BF] convert_tractogram fix
* :ghissue:`3108`: enabled trx support with correct header
* :ghissue:`3107`: enabled trx support for viz
* :ghissue:`2994`: DKI masking
* :ghissue:`3033`: [RF] fix dki mask for nlls
* :ghissue:`3104`: Dkimaskfix
* :ghissue:`3106`: volume slices visibility fixed
* :ghissue:`3102`: Bugfix for peaks slices and synchronization.
* :ghissue:`2281`: Black Output for pam5 file with dipy_horizon
* :ghissue:`3078`: return S0 from dki fit
* :ghissue:`3101`: [BF] Uniformize cython version
* :ghissue:`3097`: Feature/surface
* :ghissue:`2719`: pytest and cdef functions
* :ghissue:`3048`: [TEST] Adds support of cython for pytest
* :ghissue:`3053`: [NF] Add workflow to convert tensors in different formats
* :ghissue:`3073`: [NF] Add DSI workflow
* :ghissue:`3099`: [DOC] fix some typo [ci skip]
* :ghissue:`3098`: Removing tensorflow addon from DL models
* :ghissue:`2973`: Tab names for slice tabs as file names.
* :ghissue:`3081`: NF: Adding N4 bias correction deep learning model
* :ghissue:`3092`: Feature: volume synchronizing
* :ghissue:`3093`: Can I use a different sort of dataset and also what if I don't have a bval , I use . mat images format PATCH2Self
* :ghissue:`3059`: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors
* :ghissue:`3090`: RF - changed memory view to double* trilinear_interpolation_4d
* :ghissue:`3080`: Adding SH basis legacy option support to peaks_from_model
* :ghissue:`3085`: Viz Tests failing
* :ghissue:`3087`: backward compatibility fixed
* :ghissue:`3088`: [TEST] Pin pytest
* :ghissue:`3074`: Horizon for large datasets - concerns regarding np.unique
* :ghissue:`3075`: Horizon - 4D data support - slicing on the 4-th dim
* :ghissue:`3084`: fixed 4d slice issue
* :ghissue:`3083`: Np.unique check removed.
* :ghissue:`3082`: Add Fedora installation instructions [ci skip]
* :ghissue:`3065`: Add s390x test workflow
* :ghissue:`3076`: [CI] Update scientific-python/upload-nightly-action to 0.5.0
* :ghissue:`3070`: [DOC] Fix installation link in README  [ci skip]
* :ghissue:`3069`: [DOC] Fix DTI Tutorial [ci skip]
* :ghissue:`3066`: Dipy website incorrect image
* :ghissue:`3063`: [RF] remove cpdef in PmfGen
* :ghissue:`3054`: [DOC] Fix some links [ci skip]
* :ghissue:`3060`: Bump codecov/codecov-action from 3 to 4
* :ghissue:`3061`: [OPT] Enable openmp for macOS wheel and CI's
* :ghissue:`3057`:   Using the atlas HCP1065 in DIPY
* :ghissue:`3055`: [RF] replace Bunch by Enum
* :ghissue:`3049`: [MTN] code cleaning: remove some dependencies version checking
* :ghissue:`3050`: [RF] Move ``dipy.boots.resampling`` to  ``dipy.stats.resampling``
* :ghissue:`3051`: [RF] Remove dipy.io.bvectxt module
* :ghissue:`3052`: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874
* :ghissue:`2789`: Horizon image's dtype validation
* :ghissue:`3047`: "Editable" installation broken
* :ghissue:`3045`: [DOC] fix `multi_shell_fiber_response` docstring array dims [ci skip]
* :ghissue:`3041`: [NF] Add convert tractograms flow
* :ghissue:`3040`: [BW] Remove some python2 reference
* :ghissue:`3039`: [TEST] Add setup_module and teardown_module
* :ghissue:`3038`: [NF] Update `dipy_info`: allow tractogram files format
* :ghissue:`3043`: d/d/t/test_data.py: endian independent dtype.
* :ghissue:`3042`: pyproject.toml: no cython at run time.
* :ghissue:`3027`: [NF] Add Concatenate tracks workflows
* :ghissue:`3035`: If I want to use  6D array in "actor.odf_slicer", how can i do?
* :ghissue:`2993`: Add conversion utility between DIPY and MRtrix3 spherical harmonic basis
* :ghissue:`3008`: NF: add SH basis conversion between dipy and mrtrix3
* :ghissue:`3025`: [TEST] Manage http errors for stateful tractograms
* :ghissue:`3031`: Bugfix: Horizon image's dtype validation
* :ghissue:`3032`: Consider moving your nightly wheel away from the scipy-wheel-nightly (old location) to scientific-python-nightly-wheels
* :ghissue:`3021`: [MTN] Remove 3.8 Ci's
* :ghissue:`3003`: DIPY installation raises Cython warnings
* :ghissue:`3026`: [RF] Fix cython 3 warnings
* :ghissue:`2852`: Different behavior regarding color channels of horizon
* :ghissue:`2378`: A novice's request for advice on loading very large tractograms (.tck)
* :ghissue:`2064`: How to register MR to CT of the same person?
* :ghissue:`2601`: read_bvals_bvecs can't read double volume dwi
* :ghissue:`3022`: [DOC] Fix logo size and link [ci skip]
* :ghissue:`3013`: Added Fibonacci spiral and test for it
* :ghissue:`3020`: load_nifti import doesn't work if using submodule directly
* :ghissue:`3019`: DOC: Fix link to toolchain roadmap page in `README`
* :ghissue:`3012`: DOC: Document observance for Scientific Python min supported versions
* :ghissue:`3018`: Bump actions/download-artifact from 3 to 4
* :ghissue:`3017`: Bump actions/upload-artifact from 3 to 4
* :ghissue:`3014`: Update release1.8.rst
* :ghissue:`1525`: Clang-omp moved to boneyard on brew

**DIPY 1.8.0** is now available. New features include:

- 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.

====================================

 Release notes for DIPY version 1.7
====================================

**DIPY 1.7.0** is now available. New features include:

- 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.

GitHub stats for 2023/01/16 - 2023/04/23 (tag: 1.6.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 21 authors contributed 496 commits.

* Ariel Rokem
* Bramsh Qamar
* Charles Poirier
* Dogu Baran Aydogan
* Eleftherios Garyfallidis
* Etienne St-Onge
* Francois Rheault
* Gabriel Girard
* Javier Guaje
* Jong Sung Park
* Martino Pilia
* Mitesh Gulecha
* Rahul Ubale
* Sam Coveney
* Serge Koudoro
* Shilpi
* Tom Dela Haije
* Yaroslav Halchenko
* karp2601
* lb-97
* ujjwal-shekhar

We closed a total of 87 issues, 34 pull requests and 53 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (34):

* :ghpull:`2765`: Sphinx-gallery integration
* :ghpull:`2788`: Remove NoseTester
* :ghpull:`2768`: BundleWarp, streamline-based nonlinear registration of white matter tracts
* :ghpull:`2749`: adding a new getitem method
* :ghpull:`2744`: Horizon Tabs
* :ghpull:`2785`: EVAC+ workflow
* :ghpull:`2540`: Updates the default value of rm_small_clusters variable in slr_with_qbx function
* :ghpull:`2609`: NF: DKI+ constraints
* :ghpull:`2596`: NF - Parallel Transport Tractography (PTT)
* :ghpull:`2740`: Integration of Denoising Method for DWI with 1D CNN
* :ghpull:`2773`: Including EVAC+ and util function
* :ghpull:`2783`: Fix test_roi_images
* :ghpull:`2782`: [MTN] Fix CI codecov upload
* :ghpull:`2780`: Added option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff
* :ghpull:`2778`: BF: QBX and merge clusters should return streamlines
* :ghpull:`2767`: NF - add utility functions to fast_numpy
* :ghpull:`2626`: Adding Synb0
* :ghpull:`2763`: Update dki.py
* :ghpull:`2751`: [ENH] Asymmetric peak_directions
* :ghpull:`2762`: Remove Python 3.7 from CI
* :ghpull:`2753`: Update adaptive_soft_matching.py
* :ghpull:`2722`: fixed pca for features > samples, and fixed pca_noise_estimate
* :ghpull:`2741`: Fixing solve_qp error
* :ghpull:`2739`: codespell: config, workflow, typos fixed
* :ghpull:`2590`: Fast Streamline Search algorithm implementation
* :ghpull:`2733`: Update SynRegistrationFlow for #2648
* :ghpull:`2723`: TRX integration, requires new attributes for SFT
* :ghpull:`2727`: Fix EXTRAS_REQUIRE
* :ghpull:`2725`: DOC - Update RUMBA-SD data requirement
* :ghpull:`2716`: NF - Added cython utility functions
* :ghpull:`2717`: fixed bug for non-linear fitting with masks
* :ghpull:`2628`: resolve some CI's script typo
* :ghpull:`2713`: Empty vtk support
* :ghpull:`2625`: [Upcoming] Release 1.6.0

Issues (53):

* :ghissue:`2537`: Importing an example in another example - doc
* :ghissue:`1778`: jupyter notebooks from examples
* :ghissue:`720`: Auto-convert the examples into IPython notebooks
* :ghissue:`1990`: [WIP] Sphinx-Gallery integration
* :ghissue:`2765`: Sphinx-gallery integration
* :ghissue:`2788`: Remove NoseTester
* :ghissue:`2768`: BundleWarp, streamline-based nonlinear registration of white matter tracts
* :ghissue:`1073`: Add a method to slice gtab using bvals (Eg : gtab[bvals>200])
* :ghissue:`2749`: adding a new getitem method
* :ghissue:`2744`: Horizon Tabs
* :ghissue:`2785`: EVAC+ workflow
* :ghissue:`2530`: slr_with_qbx breaks when bundle has only one streamline
* :ghissue:`2540`: Updates the default value of rm_small_clusters variable in slr_with_qbx function
* :ghissue:`2609`: NF: DKI+ constraints
* :ghissue:`2596`: NF - Parallel Transport Tractography (PTT)
* :ghissue:`2756`: Remove unused inplace param from gibbs_removal()
* :ghissue:`2754`: [Question] dipy/denoise/gibbs.py
* :ghissue:`2740`: Integration of Denoising Method for DWI with 1D CNN
* :ghissue:`2773`: Including EVAC+ and util function
* :ghissue:`2783`: Fix test_roi_images
* :ghissue:`2782`: [MTN] Fix CI codecov upload
* :ghissue:`2775`: NF - Add option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff(.)
* :ghissue:`2780`: Added option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff
* :ghissue:`2778`: BF: QBX and merge clusters should return streamlines
* :ghissue:`2767`: NF - add utility functions to fast_numpy
* :ghissue:`2626`: Adding Synb0
* :ghissue:`2770`: BF - update viz.py
* :ghissue:`2763`: Update dki.py
* :ghissue:`2751`: [ENH] Asymmetric peak_directions
* :ghissue:`2762`: Remove Python 3.7 from CI
* :ghissue:`2753`: Update adaptive_soft_matching.py
* :ghissue:`2722`: fixed pca for features > samples, and fixed pca_noise_estimate
* :ghissue:`2750`: Adding tests for gradient.py.
* :ghissue:`2741`: Fixing solve_qp error
* :ghissue:`2745`: Dipy Segmentation Core Dumped - Windows.Record
* :ghissue:`2742`: ValueError: slice step cannot be zero
* :ghissue:`2739`: codespell: config, workflow, typos fixed
* :ghissue:`2590`: Fast Streamline Search algorithm implementation
* :ghissue:`2733`: Update SynRegistrationFlow for #2648
* :ghissue:`2723`: TRX integration, requires new attributes for SFT
* :ghissue:`2729`: Numpy Version Incompatibility, AttributeError in dipy.align
* :ghissue:`2726`: Setup broken on Python 3.10.9 setuptools 67.2.0
* :ghissue:`2727`: Fix EXTRAS_REQUIRE
* :ghissue:`2725`: DOC - Update RUMBA-SD data requirement
* :ghissue:`2707`: Fixdenoise
* :ghissue:`2575`: [WIP]  Define curvature and stepsize as default parameter instead of max_angle for tractography
* :ghissue:`2414`: AffineMap.transform with option: interpolation='nearest' returns: "TypeError: No matching signature found"
* :ghissue:`2716`: NF - Added cython utility functions
* :ghissue:`2717`: fixed bug for non-linear fitting with masks
* :ghissue:`2628`: resolve some CI's script typo
* :ghissue:`2713`: Empty vtk support
* :ghissue:`2599`: Support empty ArraySequence in transform_streamlines
* :ghissue:`2625`: [Upcoming] Release 1.6.0

====================================

 Release notes for DIPY version 1.6
====================================

- 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.

GitHub stats for 2022/03/11 - 2023/01/12 (tag: 1.5.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 15 authors contributed 242 commits.

* Ariel Rokem
* David Romero-Bascones
* Deneb Boito
* Eleftherios Garyfallidis
* Emmanuelle Renauld
* Eric Larson
* Francois Rheault
* Jacob Roberts
* Jon Haitz Legarreta Gorroño
* Malinda Dilhara
* Omar Ocegueda
* Sam Coveney
* Serge Koudoro
* Shreyas Fadnavis
* Tom Dela Haije

We closed a total of 116 issues, 41 pull requests and 75 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (41):

* :ghpull:`2710`: small fixes for tutorials
* :ghpull:`2711`: [FIX] use tempfile module instead of nibabel for TemporaryDirectory
* :ghpull:`2702`: One more small fix to the hcp fetcher.
* :ghpull:`2704`: MAINT: Fixes for 3.11 and sdist
* :ghpull:`2701`: FIX: Don't print a progbar for downloading unless you need to.
* :ghpull:`2700`: [FIX] incompatible type in numpy array
* :ghpull:`2694`: NF: Add RUMBA-SD reconstruction workflow
* :ghpull:`2697`: NF: Adds a fetcher for HCP data.
* :ghpull:`2692`: RF: Improve multi-shell RUMBA test WM response parameterization
* :ghpull:`2693`: TEST: Fix `Node.js` warnings linked to GitHub actions
* :ghpull:`2687`: DOC: Fix typos in SH theory documentation page
* :ghpull:`2690`: STYLE: Remove unnecessary b-val print in CSD reconstruction flow
* :ghpull:`2688`: DOC: Document Dirac delta generation method missing member
* :ghpull:`2683`: DOC: Adds missing documentation for a kwarg.
* :ghpull:`2668`: ENH: Make the DTI fit CLI metric saving message accurate
* :ghpull:`2674`: Improve doc (tensor values' order)
* :ghpull:`2670`: ENH: Allow non-default parameters to `Patch2Self` CLI
* :ghpull:`2672`: DOC: Miscellaneous docstring fixes
* :ghpull:`2669`: DOC: Remove inaccurate `patch2self` docstring default values
* :ghpull:`2664`: DOC: Fix DTI fit CLI docstring
* :ghpull:`2553`: NF: Unbiased groupwise linear bundle registration
* :ghpull:`2369`: Transform points with DiffeormorphicMap
* :ghpull:`2631`: [FIX] Allow patch size parameter to be an int on denoise Workflow
* :ghpull:`2630`: [DOC] Remove search index
* :ghpull:`2629`: [FIX ] Handle save VTP
* :ghpull:`2618`: Use np.linalg.multi_dot instead of multiple np.dot routines
* :ghpull:`2606`: STYLE: Fix miscellaneous Python warnings
* :ghpull:`2600`: Pin Ray
* :ghpull:`2531`: NF: MAP+ constraints
* :ghpull:`2589`: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module
* :ghpull:`2577`: Add positivity constraints to QTI
* :ghpull:`2595`: Temporary skip Cython 0.29.29
* :ghpull:`2591`: STYLE: Avoid array-like mutable default argument values
* :ghpull:`2592`: STYLE: Fix miscellaneous Python warnings
* :ghpull:`2579`: Generalized PCA to less than 3 spatial dims
* :ghpull:`2584`: transform_streamlines changes dtype to float64
* :ghpull:`2566`: [FIX] Update tests for the deprecated `dipy.io.bvectxt` module
* :ghpull:`2581`: Fix logger in SFT
* :ghpull:`2580`: DOC: Fix typos and grammar
* :ghpull:`2576`: DOC: Documentation fixes
* :ghpull:`2568`: DOC: Fix the docstring of `write_mapping`

Issues (75):

* :ghissue:`2710`: small fixes for tutorials
* :ghissue:`2711`: [FIX] use tempfile module instead of nibabel for TemporaryDirectory
* :ghissue:`2709`: DiffeomorphicMap object on github not the same as recent release
* :ghissue:`2708`: Provide the dataset of this code
* :ghissue:`2699`: WIP: Single shell/noreg redux
* :ghissue:`2702`: One more small fix to the hcp fetcher.
* :ghissue:`2704`: MAINT: Fixes for 3.11 and sdist
* :ghissue:`2701`: FIX: Don't print a progbar for downloading unless you need to.
* :ghissue:`2700`: [FIX] incompatible type in numpy array
* :ghissue:`2694`: NF: Add RUMBA-SD reconstruction workflow
* :ghissue:`2696`: Port HCP fetcher from pyAFQ into here
* :ghissue:`2697`: NF: Adds a fetcher for HCP data.
* :ghissue:`2692`: RF: Improve multi-shell RUMBA test WM response parameterization
* :ghissue:`2693`: TEST: Fix `Node.js` warnings linked to GitHub actions
* :ghissue:`1418`: Adding parallel_voxel_fit decorator
* :ghissue:`2687`: DOC: Fix typos in SH theory documentation page
* :ghissue:`2690`: STYLE: Remove unnecessary b-val print in CSD reconstruction flow
* :ghissue:`2688`: DOC: Document Dirac delta generation method missing member
* :ghissue:`2683`: DOC: Adds missing documentation for a kwarg.
* :ghissue:`2679`: Problems with a .nii.gz file when loading and floating
* :ghissue:`2676`: Does ```convert_sh_to_legacy``` work as intended ?
* :ghissue:`2668`: ENH: Make the DTI fit CLI metric saving message accurate
* :ghissue:`2674`: Improve doc (tensor values' order)
* :ghissue:`2670`: ENH: Allow non-default parameters to `Patch2Self` CLI
* :ghissue:`2673`: ENH: Doc: DTI format
* :ghissue:`2667`: Defaults for Patch2Self
* :ghissue:`2672`: DOC: Miscellaneous docstring fixes
* :ghissue:`2669`: DOC: Remove inaccurate `patch2self` docstring default values
* :ghissue:`2662`: Update cmd_line dipy_fit_dti
* :ghissue:`2664`: DOC: Fix DTI fit CLI docstring
* :ghissue:`2658`: Any chance of arm64 wheels for Mac / Python 3.10?
* :ghissue:`2659`: Angle var
* :ghissue:`2649`: IVIM VarPro fitting running error
* :ghissue:`2553`: NF: Unbiased groupwise linear bundle registration
* :ghissue:`2424`: Transforming individual points with SDR
* :ghissue:`2327`: Diffeomorphic transformation of coordinates
* :ghissue:`2313`: deform_streamlines for wholebrain tractogram doesn't function properly
* :ghissue:`936`: WIP: coordinate mapping with DiffeomorphicMap
* :ghissue:`2369`: Transform points with DiffeormorphicMap
* :ghissue:`2616`: dti TensorModel fitting issue
* :ghissue:`2627`: Free-Water Analysis Gradient Table Error
* :ghissue:`2635`: get_flexi_tvis_affine(tvis_hdr, nii_aff)
* :ghissue:`2634`: Fix small difference between pdfs dense 2d/3d
* :ghissue:`2559`: CLI denoise patch_size error
* :ghissue:`2631`: [FIX] Allow patch size parameter to be an int on denoise Workflow
* :ghissue:`2564`: Search, index, module links not working in the doc
* :ghissue:`2630`: [DOC] Remove search index
* :ghissue:`2572`: Saving vtp file error
* :ghissue:`2629`: [FIX ] Handle save VTP
* :ghissue:`2622`: Error with Illustrating Electrostatic Repulsion
* :ghissue:`2618`: Use np.linalg.multi_dot instead of multiple np.dot routines
* :ghissue:`2617`: DKI model fit shape broadcast error
* :ghissue:`2606`: STYLE: Fix miscellaneous Python warnings
* :ghissue:`2602`: Dear experts, how can I set different number of fiber tracks before generating streamlines?
* :ghissue:`2603`: Dear experts, how to save dti_peaks?
* :ghissue:`2600`: Pin Ray
* :ghissue:`2531`: NF: MAP+ constraints
* :ghissue:`2587`: Thread safety concerns with reliance on `nibabel.tmpdirs.InTemporaryDirectory`
* :ghissue:`2589`: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module
* :ghissue:`2577`: Add positivity constraints to QTI
* :ghissue:`2450`: [NF] New tracking Algorithm:  Parallel Transport Tractography (PTT)
* :ghissue:`2594`: DIPY compilation fails with the last release of cython (0.29.29)
* :ghissue:`2595`: Temporary skip Cython 0.29.29
* :ghissue:`2591`: STYLE: Avoid array-like mutable default argument values
* :ghissue:`2592`: STYLE: Fix miscellaneous Python warnings
* :ghissue:`2579`: Generalized PCA to less than 3 spatial dims
* :ghissue:`2584`: transform_streamlines changes dtype to float64
* :ghissue:`2566`: [FIX] Update tests for the deprecated `dipy.io.bvectxt` module
* :ghissue:`2581`: Fix logger in SFT
* :ghissue:`2580`: DOC: Fix typos and grammar
* :ghissue:`2576`: DOC: Documentation fixes
* :ghissue:`2573`: Cannot Import "Feature" From "dipy.segment.metric"
* :ghissue:`2568`: DOC: Fix the docstring of `write_mapping`
* :ghissue:`2567`: This should be a `1`
* :ghissue:`2565`: compress_streamlines() not available anymore

===================================

 Release notes for DIPY version 1.5
===================================

GitHub stats for 2021/05/06 - 2022/03/10 (tag: 1.4.1)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 22 authors contributed 573 commits.

* Ariel Rokem
* Dan Bullock
* David Romero-Bascones
* Derek Pisner
* Eleftherios Garyfallidis
* Eric Larson
* Francis Jerome
* Francois Rheault
* Gabriel Girard
* Giulia Bertò
* Javier Guaje
* Jon Haitz Legarreta Gorroño
* Joshua Newton
* Kenji Marshall
* Leevi Kerkela
* Leon Weninger
* Lucas Da Costa
* Nasim Anousheh
* Rafael Neto Henriques
* Sam Coveney
* Serge Koudoro
* Shreyas Fadnavis

We closed a total of 200 issues, 72 pull requests and 128 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (72):

* :ghpull:`2561`: [FIX] Motion correction tutorial
* :ghpull:`2520`: Resdnn inference
* :ghpull:`2558`: BUG: Fix errant warning about starting_affine
* :ghpull:`2557`: MAINT: Fix version
* :ghpull:`2556`: [FIX] Update `dipy.segment` tutorials
* :ghpull:`2554`: Support .vtp files
* :ghpull:`2555`: Limit `peaks_from_model` number of processes in examples
* :ghpull:`2539`: Adds utilities for embarassingly parallel loops.
* :ghpull:`2545`: Stateful Tractogram DPS and DPP keys ordering
* :ghpull:`2548`: Add timeout + concurrency to GHA
* :ghpull:`2549`: [ENH] Clarify reconst_sh tutorial
* :ghpull:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow
* :ghpull:`2551`: [MNT] Update mininal dependencies version
* :ghpull:`2536`: Random colors fix in horizon
* :ghpull:`2533`: [FIX] Docstring cleaning: wrong underline length...
* :ghpull:`2342`: NF:  q-space trajectory imaging
* :ghpull:`2512`: Masking for affine registration
* :ghpull:`2526`: TEST: Filter legacy SH bases warnings in tests
* :ghpull:`2534`: TEST: Remove unnecessary `main` method definition in tests
* :ghpull:`2532`: STYLE: Remove unused import statements
* :ghpull:`2529`: STYLE: Remove unused import statements
* :ghpull:`2528`: TEST: Remove legacy `nose`-related dead testing code
* :ghpull:`2527`: TEST: Fix intermittent RUMBA test check failure
* :ghpull:`2493`: Fury dependency resolution
* :ghpull:`2522`: ENH: Miscellaneous cleanup
* :ghpull:`2521`: DOC: Use GitHub actions status badge in README
* :ghpull:`2420`: Documentation corrections
* :ghpull:`2482`: ENH: Improve SH bases warning messages
* :ghpull:`2423`: NF: rumba reconst
* :ghpull:`2518`: Migrations from Azure Pipeline to Github Actions
* :ghpull:`2515`: Default to False output for null streamlines in streamline_near_roi
* :ghpull:`2513`: [MNT] Drop distutils
* :ghpull:`2506`: Horizon FURY update
* :ghpull:`2510`: Optimize sfm (reboot)
* :ghpull:`2487`: ENH: Better error message
* :ghpull:`2442`: [NF] Add Motion correction workflow
* :ghpull:`2470`: Add utilities functions:  radius curvature <--> maximum deviation angle
* :ghpull:`2485`: DOC: Small updates.
* :ghpull:`2481`: ENH: Import ABCs from `collections.abc`
* :ghpull:`2480`: STYLE: Make `sklearn` import warning messages consistent
* :ghpull:`2478`: ENH: Deal appropriately with user warnings
* :ghpull:`2479`: STYLE: Improve style in misc files
* :ghpull:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings
* :ghpull:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning
* :ghpull:`2472`: ENH: Return unique invalid streamline removal indices
* :ghpull:`2471`: DOC: Fix coding style guideline link
* :ghpull:`2468`: [MNT] Use windows-latest on azure pipeline
* :ghpull:`2467`: [ENH] Add fit_method option in DTI and DKI CLI
* :ghpull:`2466`: deprecate dipy.io.bvectxt module
* :ghpull:`2453`: make it compatible when number of volume is 2
* :ghpull:`2413`: Azure pipeline: from ubuntu 1604 to 2004
* :ghpull:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors
* :ghpull:`2444`: [DOC] : Added citation for IVIM dataset
* :ghpull:`2434`: MAINT: Update import from ndimage
* :ghpull:`2435`: BUG: Backward compat support for pipeline
* :ghpull:`2436`: MAINT: Bump tolerance
* :ghpull:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py`
* :ghpull:`2374`: ROIs visualizer
* :ghpull:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling
* :ghpull:`2417`: OPT: Initialize `Shape` struct
* :ghpull:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols'
* :ghpull:`2406`: Manage Approx_polygon_track with repeated points
* :ghpull:`2411`: [FIX] `c_compress_streamline` discard identical points
* :ghpull:`2416`: OPT: Prefer using a typed index to get the PMF value
* :ghpull:`2415`: Implementation multi_voxel_fit progress bar
* :ghpull:`2410`: [ENH] Improve Shore Tests
* :ghpull:`2409`: NF - Sample PMF for an input position and direction
* :ghpull:`2405`: Small correction on KFA
* :ghpull:`2407`: from random to deterministic test for deform_streamlines
* :ghpull:`2392`: Add decomposition
* :ghpull:`2389`: [Fix] bundles_distances_mdf asymmetric values
* :ghpull:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.

Issues (128):

* :ghissue:`2561`: [FIX] Motion correction tutorial
* :ghissue:`2123`: WIP: Residual Deep NN
* :ghissue:`2520`: Resdnn inference
* :ghissue:`2558`: BUG: Fix errant warning about starting_affine
* :ghissue:`2557`: MAINT: Fix version
* :ghissue:`2489`: MAINT: Get Python 3.10 binaries up on scipy-wheels-nightly
* :ghissue:`2556`: [FIX] Update `dipy.segment` tutorials
* :ghissue:`2554`: Support .vtp files
* :ghissue:`2525`: Support Opening `.vtp` files
* :ghissue:`2555`: Limit `peaks_from_model` number of processes in examples
* :ghissue:`2539`: Adds utilities for embarassingly parallel loops.
* :ghissue:`2509`: Easy robustness for streamline_near_roi and near_roi for empty streamlines?
* :ghissue:`2543`: StatefulTractogram.are_compatible compare data_per_point keys as list instead of set
* :ghissue:`2545`: Stateful Tractogram DPS and DPP keys ordering
* :ghissue:`2548`: Add timeout + concurrency to GHA
* :ghissue:`2549`: [ENH] Clarify reconst_sh tutorial
* :ghissue:`2546`: Confusing import in 'reconst_sh`
* :ghissue:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow
* :ghissue:`2542`: DTI workflow should allow user-defined fitting method
* :ghissue:`2551`: [MNT] Update mininal dependencies version
* :ghissue:`2477`: Numpy min dependency update
* :ghissue:`2541`: Issue with coverage and pytests for numpy.min()
* :ghissue:`2507`: kernel died when use dipy.viz
* :ghissue:`2536`: Random colors fix in horizon
* :ghissue:`2533`: [FIX] Docstring cleaning: wrong underline length...
* :ghissue:`2422`: WIP-Adding math in SLR tutorial
* :ghissue:`2342`: NF:  q-space trajectory imaging
* :ghissue:`2512`: Masking for affine registration
* :ghissue:`1969`: imaffine mask support
* :ghissue:`2526`: TEST: Filter legacy SH bases warnings in tests
* :ghissue:`2456`: Horizon tests failing
* :ghissue:`2534`: TEST: Remove unnecessary `main` method definition in tests
* :ghissue:`2532`: STYLE: Remove unused import statements
* :ghissue:`2524`: Add concurrency + timeout to Github Actions (GHA)
* :ghissue:`2529`: STYLE: Remove unused import statements
* :ghissue:`2528`: TEST: Remove legacy `nose`-related dead testing code
* :ghissue:`2527`: TEST: Fix intermittent RUMBA test check failure
* :ghissue:`2493`: Fury dependency resolution
* :ghissue:`2522`: ENH: Miscellaneous cleanup
* :ghissue:`2521`: DOC: Use GitHub actions status badge in README
* :ghissue:`2420`: Documentation corrections
* :ghissue:`2482`: ENH: Improve SH bases warning messages
* :ghissue:`2449`: Nonsense deprecation warning
* :ghissue:`2423`: NF: rumba reconst
* :ghissue:`2179`: NF: Complete masking implementation in affine registration with MI
* :ghissue:`2518`: Migrations from Azure Pipeline to Github Actions
* :ghissue:`2492`: Move to GitHub actions / reusable actions
* :ghissue:`2515`: Default to False output for null streamlines in streamline_near_roi
* :ghissue:`2497`: Remove python 3.6 from Azure pipelines
* :ghissue:`2495`: Remove Distutils (deprecated)
* :ghissue:`2513`: [MNT] Drop distutils
* :ghissue:`2506`: Horizon FURY update
* :ghissue:`2305`: [WIP] Brain Tumor Image Segmentation Code
* :ghissue:`2499`: Problem generating Connectivity Matrix: "Slice step cannot be zero"
* :ghissue:`2510`: Optimize sfm (reboot)
* :ghissue:`2488`: Minimize memory footprint whereever possible, add joblib support for …
* :ghissue:`2504`: Why are there many small dots on the fwdwi image?
* :ghissue:`2502`: Can i read specific b-values from my own multishell data?
* :ghissue:`2500`: MAP issue
* :ghissue:`2490`: [BUG] MRI-CT alignment failure
* :ghissue:`2487`: ENH: Better error message
* :ghissue:`2402`: Dipy 1.4.1 breaks nipype.interfaces.dipy.dipy_to_nipype_interface
* :ghissue:`2486`: Wrong doc in interpolation
* :ghissue:`2442`: [NF] Add Motion correction workflow
* :ghissue:`2470`: Add utilities functions:  radius curvature <--> maximum deviation angle
* :ghissue:`2485`: DOC: Small updates.
* :ghissue:`2484`: [ENH] Add grid search to `AffineRegistration.optimize`
* :ghissue:`2483`: [DOC] Stable/Latest Documentation Structure
* :ghissue:`2481`: ENH: Import ABCs from `collections.abc`
* :ghissue:`2480`: STYLE: Make `sklearn` import warning messages consistent
* :ghissue:`2478`: ENH: Deal appropriately with user warnings
* :ghissue:`2479`: STYLE: Improve style in misc files
* :ghissue:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings
* :ghissue:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning
* :ghissue:`2472`: ENH: Return unique invalid streamline removal indices
* :ghissue:`2471`: DOC: Fix coding style guideline link
* :ghissue:`2468`: [MNT] Use windows-latest on azure pipeline
* :ghissue:`2467`: [ENH] Add fit_method option in DTI and DKI CLI
* :ghissue:`2463`: DTI RESTORE on the CLI
* :ghissue:`2466`: deprecate dipy.io.bvectxt module
* :ghissue:`2460`: Deprecate and Remove dipy.io.bvectxt
* :ghissue:`2429`: random_colors flag in dipy_horizon does not work as before
* :ghissue:`2461`: Patch2Self: Less than 10 3D Volumes Bug
* :ghissue:`2464`: Typo on the homepage
* :ghissue:`2453`: make it compatible when number of volume is 2
* :ghissue:`2457`: Choosing sigma_diff and radius parameters for SyN registration
* :ghissue:`2413`: Azure pipeline: from ubuntu 1604 to 2004
* :ghissue:`2454`: Can I show fiber with vtk?
* :ghissue:`2446`: Use of bitwise or with non-bool inputs results in ufunc 'bitwise_or' error
* :ghissue:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors
* :ghissue:`2444`: [DOC] : Added citation for IVIM dataset
* :ghissue:`2443`: Citation for IVIM dataset not present in docs
* :ghissue:`2434`: MAINT: Update import from ndimage
* :ghissue:`2441`: Horizon error - disk position outside the slider line
* :ghissue:`2435`: BUG: Backward compat support for pipeline
* :ghissue:`2436`: MAINT: Bump tolerance
* :ghissue:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py`
* :ghissue:`2430`: dipy.align.reslice
* :ghissue:`2431`: dipy.align.reslice interpolation order for downsampling
* :ghissue:`2432`: How to apply MI metric in dipy？
* :ghissue:`2374`: ROIs visualizer
* :ghissue:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling
* :ghissue:`2417`: OPT: Initialize `Shape` struct
* :ghissue:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols'
* :ghissue:`2406`: Manage Approx_polygon_track with repeated points
* :ghissue:`2314`: Approx_polygon_track with repeated points gives an error
* :ghissue:`2411`: [FIX] `c_compress_streamline` discard identical points
* :ghissue:`1805`: `c_compress_streamline` keeps identical points when it shouldn't
* :ghissue:`2418`: kernel failure when importing mask from dipy.segment
* :ghissue:`2416`: OPT: Prefer using a typed index to get the PMF value
* :ghissue:`2415`: Implementation multi_voxel_fit progress bar
* :ghissue:`2410`: [ENH] Improve Shore Tests
* :ghissue:`365`: Code review items for `dipy.reconst.shore`
* :ghissue:`2409`: NF - Sample PMF for an input position and direction
* :ghissue:`2404`: Change affine in StatefulTractogram
* :ghissue:`2405`: Small correction on KFA
* :ghissue:`2407`: from random to deterministic test for deform_streamlines
* :ghissue:`2392`: Add decomposition
* :ghissue:`717`: Download each shell of the CENIR data separately?
* :ghissue:`2209`: _pytest.pathlib.ImportPathMismatchError:
* :ghissue:`1934`: Random lpca denoise
* :ghissue:`2312`: DIPY open group meetings, Spring 2021
* :ghissue:`2383`: error in mcsd model fitting (DCPError)
* :ghissue:`2391`: error performing cross-validation on diffusion HCP data
* :ghissue:`2393`: Add a function to read streamline from the result generated by the command "probtrackx2" in FMRIB's Diffusion Toolbox
* :ghissue:`2389`: [Fix] bundles_distances_mdf asymmetric values
* :ghissue:`2310`: `bundles_distances_mdf` asymmetric values
* :ghissue:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.

=====================================

 Release notes for DIPY version 1.4.1
=====================================

- 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.

GitHub stats for 2021/03/14 - 2021/05/05 (tag: 1.4.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 11 authors contributed 153 commits.

* Ariel Rokem
* Bramsh Qamar Chandio
* David Romero-Bascones
* Eleftherios Garyfallidis
* Etienne St-Onge
* Felix Liu
* Gabriel Girard
* John Kruper
* Nasim Anousheh
* Serge Koudoro
* Shreyas Fadnavis

We closed a total of 89 issues, 28 pull requests and 61 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (28):

* :ghpull:`2367`: [Upcoming] Release 1.4.1
* :ghpull:`2387`: added all examples of CST and updated AFQ file name
* :ghpull:`2386`: Adding CST_L back in Bundle Segmentation Tutorial
* :ghpull:`2375`: Expanding Bundle Segmentation Tutorial
* :ghpull:`2382`: Updated docs for using P2S optimally
* :ghpull:`2385`: RF: Standardize the argument name for the number of threads/cores
* :ghpull:`2384`: RF - Removed deprecated tracking code
* :ghpull:`2351`: Updating Vec2vec_rotmat to deal with numerical issues
* :ghpull:`2381`: Adds the NIPY code of conduct to our repo.
* :ghpull:`2371`: [Fix] Add "None" options in the CLIs
* :ghpull:`2352`: RF: configure num_threads==-1 as the value to use all cores
* :ghpull:`2373`: [FIX] warning if not the same number of points
* :ghpull:`2372`: Expand patch radius if input is int
* :ghpull:`2348`: RF: Use new name for this function.
* :ghpull:`2363`: [ENH] Adding cython file(*.pyx) in documentation
* :ghpull:`2365`: [DOC]: Change defaults in Patch2Self example
* :ghpull:`2349`: [ENH] Allow for other statistics, like median, in afq_profile
* :ghpull:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays
* :ghpull:`2346`: [MNT]  Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible
* :ghpull:`2347`: Replacing Data in NLMeans Tutorial
* :ghpull:`2340`: [FIX] reactivate codecov
* :ghpull:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial
* :ghpull:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int
* :ghpull:`1648`: Mesh seeding (surface)
* :ghpull:`2337`: BF: Change patch2self defaults.
* :ghpull:`2333`: Add __str__ to GradientTable
* :ghpull:`2335`: RF: Replaces deprecated basis by its new name.
* :ghpull:`2332`: [FIX] fix tests for all new deprecated functions

Issues (61):

* :ghissue:`2375`: Expanding Bundle Segmentation Tutorial
* :ghissue:`1973`: Recobundles documentation
* :ghissue:`2382`: Updated docs for using P2S optimally
* :ghissue:`2385`: RF: Standardize the argument name for the number of threads/cores
* :ghissue:`2377`: RF: standardize the argument name for the number of threads/cores
* :ghissue:`2384`: RF - Removed deprecated tracking code
* :ghissue:`2351`: Updating Vec2vec_rotmat to deal with numerical issues
* :ghissue:`2381`: Adds the NIPY code of conduct to our repo.
* :ghissue:`2380`: Community and governance
* :ghissue:`2371`: [Fix] Add "None" options in the CLIs
* :ghissue:`2300`: NF: Add "None" options in the CLIs
* :ghissue:`2352`: RF: configure num_threads==-1 as the value to use all cores
* :ghissue:`2373`: [FIX] warning if not the same number of points
* :ghissue:`2320`: RecoBundles distances
* :ghissue:`2372`: Expand patch radius if input is int
* :ghissue:`2341`: Allow use of all threads in the gibbs ringing workflow
* :ghissue:`2348`: RF: Use new name for this function.
* :ghissue:`2353`: How to create tractogram from a multi-shell data for RecoBundles
* :ghissue:`1311`: Adding cython file(*.pyx) in documentation
* :ghissue:`2363`: [ENH] Adding cython file(*.pyx) in documentation
* :ghissue:`1302`: [DOC] cython (pyx) files are not parsed
* :ghissue:`366`: Some doc missing
* :ghissue:`2365`: [DOC]: Change defaults in Patch2Self example
* :ghissue:`1672`: Dipy Segmentation fault when visualizing
* :ghissue:`1444`: Move general registration tools into own package?
* :ghissue:`562`: Multiprocessing the tensor reconstruction
* :ghissue:`13`: Cordinate maps stuff
* :ghissue:`2324`: Dipy for VR/AR
* :ghissue:`2345`: Saving and/or importing nonlinear warps
* :ghissue:`2349`: [ENH] Allow for other statistics, like median, in afq_profile
* :ghissue:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays
* :ghissue:`423`: Use npy_intp variables instead of int and size_t to iterate over numpy arrays
* :ghissue:`837`: Should we enforce float32 in tractography results?
* :ghissue:`636`: Get a standard interface for the functions using the noise variance
* :ghissue:`861`: open mp defaults to one core, is that a good idea?
* :ghissue:`2346`: [MNT]  Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible
* :ghissue:`1895`: Cython warnings
* :ghissue:`545`: Use cnp.PyArray_DATA wherever possible
* :ghissue:`2347`: Replacing Data in NLMeans Tutorial
* :ghissue:`1847`: Replacing Data in NLMeans Tutorial
* :ghissue:`2340`: [FIX] reactivate codecov
* :ghissue:`1872`: Did we lose our coverage reporting?
* :ghissue:`1646`: Fetcher should not be under coverage
* :ghissue:`1635`: Track from mesh
* :ghissue:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial
* :ghissue:`2309`: Tractogram Header in RecoBundles Tutorial
* :ghissue:`2334`: Aphysical signal after running patch2self
* :ghissue:`1873`: ERROR while import data
* :ghissue:`2343`: Missing Python 3.9 wheels
* :ghissue:`1996`: Documentation not being rendered correctly
* :ghissue:`2311`: Accuracy of DKI measures
* :ghissue:`2274`: DKI metrics' accuracy
* :ghissue:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int
* :ghissue:`1648`: Mesh seeding (surface)
* :ghissue:`1675`: WIP: Integer indices
* :ghissue:`2316`: TranslationTransform2D Exact X-Y Shift
* :ghissue:`2337`: BF: Change patch2self defaults.
* :ghissue:`2333`: Add __str__ to GradientTable
* :ghissue:`2331`: gtab.info does not print anything
* :ghissue:`2335`: RF: Replaces deprecated basis by its new name.
* :ghissue:`2332`: [FIX] fix tests for all new deprecated functions

.. _release1.4:

====================================
 Release notes for DIPY version 1.4
====================================

GitHub stats for 2020/11/05 - 2021/03/13 (tag: 1.3.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 8 authors contributed 119 commits.

* Areesha Tariq
* Ariel Rokem
* Bramsh Qamar
* Eleftherios Garyfallidis
* Jon Haitz Legarreta Gorroño
* Philippe Karan
* Serge Koudoro
* Shreyas Fadnavis

We closed a total of 47 issues, 19 pull requests and 28 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (19):

* :ghpull:`2318`: [MAINT] Fixed Handling Negative Values for P2S
* :ghpull:`2317`: Allowing response_from_mask_msmt to take btens into account
* :ghpull:`2315`: Add weekly build to azure + update linux matrix
* :ghpull:`2307`: BUAN Documentation Typo
* :ghpull:`2278`: BUAN and RB Documentation update
* :ghpull:`2275`: [DOC]: Reconstruction CLI
* :ghpull:`2277`: [DOC] Registration CLI
* :ghpull:`2289`: Patch2Self: Denoising Diffusion MRI with Self-supervised Learning
* :ghpull:`2292`: [DOC]: Add Tracking CLI Documentation
* :ghpull:`2296`: [DOC] Fix the 'None' value in num_threads attribute
* :ghpull:`2294`: [DOC]: Remove default values from docstrings
* :ghpull:`2291`: Adds  for the dipy.align._public module
* :ghpull:`2295`: [DOC]: Fix inconsistent function parameters
* :ghpull:`2280`: DOC: Improve the denoising workflow documentation
* :ghpull:`2287`: [DOC] Remove default values from doctstrings for reconstruction methods
* :ghpull:`2286`: [DOC] fix inconsistent citation style
* :ghpull:`2284`: [DOC] Fix incorrect default output directory in doctsrings
* :ghpull:`2283`: [DOC] Fix incorrect default output directory in doctsrings
* :ghpull:`2282`: [DOC] fix minor typo

Issues (28):

* :ghissue:`2210`: Really release the memory used by arclength variable.
* :ghissue:`722`: Adding optional (GPL) dependencies to have new features
* :ghissue:`2328`: Website is down
* :ghissue:`2323`: Brain mask as a required argument to CLI
* :ghissue:`2318`: [MAINT] Fixed Handling Negative Values for P2S
* :ghissue:`2317`: Allowing response_from_mask_msmt to take btens into account
* :ghissue:`2315`: Add weekly build to azure + update linux matrix
* :ghissue:`2229`: DIPY open group meetings, Fall 2020
* :ghissue:`2307`: BUAN Documentation Typo
* :ghissue:`2098`: Q-Space Interpolation Methods
* :ghissue:`2278`: BUAN and RB Documentation update
* :ghissue:`2275`: [DOC]: Reconstruction CLI
* :ghissue:`2277`: [DOC] Registration CLI
* :ghissue:`2303`: DKI ODF
* :ghissue:`685`: (WIP) DKI PR5 - NF: DKI-ODF estimation
* :ghissue:`2289`: Patch2Self: Denoising Diffusion MRI with Self-supervised Learning
* :ghissue:`2292`: [DOC]: Add Tracking CLI Documentation
* :ghissue:`2296`: [DOC] Fix the 'None' value in num_threads attribute
* :ghissue:`2294`: [DOC]: Remove default values from docstrings
* :ghissue:`2291`: Adds  for the dipy.align._public module
* :ghissue:`2295`: [DOC]: Fix inconsistent function parameters
* :ghissue:`2280`: DOC: Improve the denoising workflow documentation
* :ghissue:`2287`: [DOC] Remove default values from doctstrings for reconstruction methods
* :ghissue:`2286`: [DOC] fix inconsistent citation style
* :ghissue:`2284`: [DOC] Fix incorrect default output directory in doctsrings
* :ghissue:`2283`: [DOC] Fix incorrect default output directory in doctsrings
* :ghissue:`2282`: [DOC] fix minor typo
* :ghissue:`2279`: Visibility of Workflow Tutorials on DIPY website

====================================

 Release notes for DIPY version 1.3
====================================

GitHub stats for 2020/09/09 - 2020/11/02 (tag: 1.2.0)

Highlight:
---------

- 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.

The following 14 authors contributed 284 commits.

* Areesha Tariq
* Ariel Rokem
* Basile Pinsard
* Bramsh Qamar
* Charles Poirier
* Eleftherios Garyfallidis
* Eric Larson
* Gregory Lee
* Jaewon Chung
* Jon Haitz Legarreta Gorroño
* Philippe Karan
* Rafael Neto Henriques
* Serge Koudoro
* Siddharth Kapoor

We closed a total of 134 issues, 49 pull requests and 85 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (49):

* :ghpull:`2181`: BUAN bundle highlight option in horizon
* :ghpull:`2223`: [NF] new linear transforms for Rigid+IsoScaling and Rigid+Scaling
* :ghpull:`2238`: [FIX] fix cython error from pre matrix
* :ghpull:`2265`: Gibbs denoising: fft only along the axis of interest
* :ghpull:`2206`: NF: Update definitions of SH bases and documentation
* :ghpull:`2266`: STYLE: minor refactoring in TissueClassifierHMRF
* :ghpull:`2255`: Modifying dti.design_matrix to take gtab.btens into account
* :ghpull:`2271`: Increase Azure pipeline timeout
* :ghpull:`2263`: [FIX] update multiple models due to cvxpy 1.1 (part2)
* :ghpull:`2259`: [Fix]  Allow read_bvals_bvecs to have 1 or 2 dwi volumes only
* :ghpull:`2264`: BF: Fix `dipy_align_syn` default value assumptions
* :ghpull:`2268`: BUG: Fix literal
* :ghpull:`2267`: BUG: Fix string literal
* :ghpull:`2262`: [FIX] update tests to respect numpy NEP 34
* :ghpull:`2244`: DOC : Denoising CLI
* :ghpull:`2119`: RecoBundles updated to read and save .trk files from Old API
* :ghpull:`2260`: [Fix] Better error handling in Diffeomorphic map `get_map`
* :ghpull:`2258`: [FIX] update Azure OSX CI + remove Azure Linux CI's
* :ghpull:`2257`: [Fix] warning if not the same number of points
* :ghpull:`2261`: [DOC]:Removed tracking evaluation section
* :ghpull:`1919`: [DOC] Add an overview of reconstruction models
* :ghpull:`2256`: update BUAN citations
* :ghpull:`2253`: Improve FFT efficiency in gibbs_removal
* :ghpull:`2240`: [ENH] Deprecate interp parameter name in AffineMap
* :ghpull:`2198`: Make single and multi tensor simulations compatible with btensors
* :ghpull:`2025`: Adds an align.api module, which provides simplified API to registration functions
* :ghpull:`2197`: Estimate smt2 metrics from mean signal kurtosis
* :ghpull:`2227`: RF: Replaces our own custom progressbar with a tqdm progressbar.
* :ghpull:`2250`: [ENH] Add parallelization to gibbs denoising
* :ghpull:`2252`: BUG: Set tau factor to parameter value in local PCA
* :ghpull:`2248`: [DOC] fetching dataset
* :ghpull:`2249`: [fix] fix value_range in HORIZON
* :ghpull:`2247`: BF: In  LiFE, set nan signals to 0.
* :ghpull:`2246`: [DOC] Replace simple backticks with double backticks
* :ghpull:`2239`: [ENH] Add inplace kwarg to gibbs_removal
* :ghpull:`2242`: maintenance of bundle_shape_similarity function
* :ghpull:`2241`: STYLE: Exclude package information file from PEP8 checks
* :ghpull:`2235`: DOC: Add tips to the documentation build section
* :ghpull:`2234`: DOC: Improve some of the links in the `info.py` file
* :ghpull:`2233`: Clarifying msmt response function docstrings
* :ghpull:`2231`: DOC: Fix HTML tag in dataset list documentation table
* :ghpull:`2221`: Robustify solve_qp for possible SolverError in one odd voxel
* :ghpull:`2226`: STYLE: Conform to `reStructuredText` syntax in examples sections
* :ghpull:`2225`: [CI] Replace Rackspace by https://anaconda.org/scipy-wheels-nightly
* :ghpull:`2224`: Replace pytest.xfail by npt.assert_raises
* :ghpull:`2220`: [DOC] move Denoising on its own section
* :ghpull:`2218`: DOC : inconsistent save_seeds documentation
* :ghpull:`2217`: Fixing numpy version rcond issue in numpy.linalg.lstsq
* :ghpull:`2211`: [FIX] used numerical indices for references

Issues (85):

* :ghissue:`2181`: BUAN bundle highlight option in horizon
* :ghissue:`2272`: DOC : Registration CLI
* :ghissue:`2223`: [NF] new linear transforms for Rigid+IsoScaling and Rigid+Scaling
* :ghissue:`2180`: [NF] add new linear transforms for Rigid+IsoScaling and Rigid+Scaling
* :ghissue:`2238`: [FIX] fix cython error from pre matrix
* :ghissue:`2265`: Gibbs denoising: fft only along the axis of interest
* :ghissue:`2206`: NF: Update definitions of SH bases and documentation
* :ghissue:`392`: mrtrix 0.3 default basis is different from mrtrix 0.2
* :ghissue:`2266`: STYLE: minor refactoring in TissueClassifierHMRF
* :ghissue:`2255`: Modifying dti.design_matrix to take gtab.btens into account
* :ghissue:`2271`: Increase Azure pipeline timeout
* :ghissue:`2054`: Discrepancy between dipy.gibbs.gibbs_removal and reisert/unring/
* :ghissue:`2263`: [FIX] update multiple models due to cvxpy 1.1 (part2)
* :ghissue:`2190`: Reconstruction with Multi-Shell Multi-Tissue CSD
* :ghissue:`2259`: [Fix]  Allow read_bvals_bvecs to have 1 or 2 dwi volumes only
* :ghissue:`2046`: read_bvals_bvecs can't read a single volume dwi
* :ghissue:`2264`: BF: Fix `dipy_align_syn` default value assumptions
* :ghissue:`2268`: BUG: Fix literal
* :ghissue:`2267`: BUG: Fix string literal
* :ghissue:`2262`: [FIX] update tests to respect numpy NEP 34
* :ghissue:`2132`: Generating ndarrays with different shapes generates NumPy warning at testing
* :ghissue:`1266`: test_mapmri_isotropic_static_scale_factor failure on OSX buildbot
* :ghissue:`1264`: FBC measures test failure on PPC
* :ghissue:`2244`: DOC : Denoising CLI
* :ghissue:`2119`: RecoBundles updated to read and save .trk files from Old API
* :ghissue:`2117`: RecoBundles workflow still using old API
* :ghissue:`2260`: [Fix] Better error handling in Diffeomorphic map `get_map`
* :ghissue:`2202`: Add error handling in Diffeomorphic map `get_map`
* :ghissue:`2258`: [FIX] update Azure OSX CI + remove Azure Linux CI's
* :ghissue:`2257`: [Fix] warning if not the same number of points
* :ghissue:`342`: Missing a warning if not the same number of points
* :ghissue:`2261`: [DOC]:Removed tracking evaluation section
* :ghissue:`2115`: Independent section on Fiber tracking evaluation not necessary
* :ghissue:`1744`: [WIP] [NF] Free Water Elimination for single-shell DTI (updated version)
* :ghissue:`1919`: [DOC] Add an overview of reconstruction models
* :ghissue:`1489`: Documentation: how to know which models support multi-shell?
* :ghissue:`2256`: update BUAN citations
* :ghissue:`2253`: Improve FFT efficiency in gibbs_removal
* :ghissue:`2240`: [ENH] Deprecate interp parameter name in AffineMap
* :ghissue:`2192`: Bringing AffineMap and DiffeomorphicMap a little closer together
* :ghissue:`2198`: Make single and multi tensor simulations compatible with btensors
* :ghissue:`2025`: Adds an align.api module, which provides simplified API to registration functions
* :ghissue:`2201`: Gradient table message error
* :ghissue:`2232`: This should be len(np.unique(gtab.bvals)) - 1 or somesuch
* :ghissue:`2197`: Estimate smt2 metrics from mean signal kurtosis
* :ghissue:`2227`: RF: Replaces our own custom progressbar with a tqdm progressbar.
* :ghissue:`2219`: Replace fetcher progress bar with tqdm
* :ghissue:`2250`: [ENH] Add parallelization to gibbs denoising
* :ghissue:`2236`: Parallelize gibbs_removal
* :ghissue:`2254`: Trackvis header saved with Dipy (nibabel) is not read  by Matlab or other tools
* :ghissue:`2252`: BUG: Set tau factor to parameter value in local PCA
* :ghissue:`2251`: localpca tau_factor is hard coded to 2.3
* :ghissue:`2248`: [DOC] fetching dataset
* :ghissue:`2249`: [fix] fix value_range in HORIZON
* :ghissue:`2243`: Unable to visualize data through dipy_horizon
* :ghissue:`2247`: BF: In  LiFE, set nan signals to 0.
* :ghissue:`2246`: [DOC] Replace simple backticks with double backticks
* :ghissue:`2239`: [ENH] Add inplace kwarg to gibbs_removal
* :ghissue:`2237`: gibbs_removal overwrites input data when inputting 3-d or 4-d data.
* :ghissue:`2245`: DOC: Fix Sphinx verbatim syntax in coding style guide
* :ghissue:`2242`: maintenance of bundle_shape_similarity function
* :ghissue:`2241`: STYLE: Exclude package information file from PEP8 checks
* :ghissue:`2235`: DOC: Add tips to the documentation build section
* :ghissue:`2234`: DOC: Improve some of the links in the `info.py` file
* :ghissue:`2222`: How can I track different streamlines in DIPY?
* :ghissue:`2233`: Clarifying msmt response function docstrings
* :ghissue:`2231`: DOC: Fix HTML tag in dataset list documentation table
* :ghissue:`2230`: TST: Assert the shape of the output based on the docstring.
* :ghissue:`2228`: Best practices for saving a tissue classifier object?
* :ghissue:`2221`: Robustify solve_qp for possible SolverError in one odd voxel
* :ghissue:`2109`: DIPY lab meetings, Spring 2020
* :ghissue:`2226`: STYLE: Conform to `reStructuredText` syntax in examples sections
* :ghissue:`2225`: [CI] Replace Rackspace by https://anaconda.org/scipy-wheels-nightly
* :ghissue:`2214`: Rackspace does not exist anymore -> Update PRE-matrix on Travis and Azure required
* :ghissue:`2224`: Replace pytest.xfail by npt.assert_raises
* :ghissue:`2220`: [DOC] move Denoising on its own section
* :ghissue:`2218`: DOC : inconsistent save_seeds documentation
* :ghissue:`2217`: Fixing numpy version rcond issue in numpy.linalg.lstsq
* :ghissue:`2216`: test_multi_shell_fiber_response failed with Numpy 1.13.3
* :ghissue:`2211`: [FIX] used numerical indices for references
* :ghissue:`2185`: Inconsistency in stating references in dti.py
* :ghissue:`2215`: problem with fetching stanford data
* :ghissue:`1762`: Font on instructions is small on mac
* :ghissue:`1354`: strange tracks
* :ghissue:`325`: streamline extraction from eudx is failing - but perhaps eudx is failing

====================================

 Release notes for DIPY version 1.2
====================================

GitHub stats for 2020/01/10 - 2020/09/08 (tag: 1.1.1)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 27 authors contributed 491 commits.

* Ariel Rokem
* Aryansh Omray
* Bramsh Qamar
* Charles Poirier
* Derek Pisner
* Eleftherios Garyfallidis
* Fabio Nery
* Francois Rheault
* Gabriel Girard
* Gregory Lee
* Jean-Christophe Houde
* Jirka Borovec
* Jon Haitz Legarreta Gorroño
* Leevi Kerkela
* Leon Weninger
* Martijn Nagtegaal
* Rafael Neto Henriques
* Sarath Chandra
* Serge Koudoro
* Shrishti Hore
* Shubham Shaswat
* Takis Panagopoulos
* Tashrif Billah
* Kunal Mehta
* svabhishek29
* Areesha Tariq
* Philippe Karan

We closed a total of 256 issues, 94 pull requests and 163 regular issues;
Pull Requests (94):

* :ghpull:`2191`: Multi-shell multi-tissue constrained spherical deconvolution
* :ghpull:`2212`: [FIX] renamed Direct Streamline Normalization tutorial title
* :ghpull:`2207`: [FIX] Horizon shader warning
* :ghpull:`2208`: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13)
* :ghpull:`2157`: BF: Fix variable may be used uninitialized warning
* :ghpull:`2205`: Add optional installs for different settings.
* :ghpull:`2204`: from Renderer to scene
* :ghpull:`2183`: _streamlines_in_mask bounds check
* :ghpull:`2203`: End of line period in sft
* :ghpull:`2142`: ENH: function to calculate size/shape parameters of b-tensors and vice-versa
* :ghpull:`2195`: [ENH] Validate streamlines pre-LiFE
* :ghpull:`2161`: Fix a memory overlap bug in multi_median (and median_otsu)
* :ghpull:`2163`: BF: Fix Cython label defined but not used warning
* :ghpull:`2174`: Improve performance of tissue classification
* :ghpull:`2168`: add fig_kwargs
* :ghpull:`2178`: Add full SH basis
* :ghpull:`2193`: BUAN_flow.rst to buan_flow.rst
* :ghpull:`2196`: [Fix] update save_vtk_streamlines and load_vtk_streamlines
* :ghpull:`2188`: [Fix] update mapmri due to cvxpy 1.1
* :ghpull:`2176`: [DOC] Update SH basis documentation
* :ghpull:`2173`: Install ssl certificate for azure pipeline windows
* :ghpull:`2171`: Gitter url update: from nipy/dipy to dipy/dipy
* :ghpull:`2154`: Bundle segmentation CLI tutorial
* :ghpull:`2162`: BF: Fix string literal comparison warning
* :ghpull:`2156`: BF: Fix Cython signed vs. unsigned integer comparison warning
* :ghpull:`2160`: TST: Change assert_equal(statement, True) to assert_(statement).
* :ghpull:`2158`: BF: Fix Cython floating point absolute value warning
* :ghpull:`2155`: [Fix] sfm RuntimeWarning
* :ghpull:`2147`: BF: Fix Cython function  override warning
* :ghpull:`2148`: BF: Fix `distutils` Python version requirement option warning
* :ghpull:`2150`: [Fix] some warning on clustering test
* :ghpull:`2149`: [Fix] some warning on stats module
* :ghpull:`2145`: Rename dipy_track command line
* :ghpull:`2152`: changed buan_flow.rst to BUAN_flow.rst
* :ghpull:`2146`: Cluster threshold parameter in dipy_buan_shapes workflow
* :ghpull:`2134`: Slicing, adding function of StatefulTractogram
* :ghpull:`2001`: Basic processing documentation for CLI.
* :ghpull:`2135`: [Fix] shm.py RuntimeWarning
* :ghpull:`2141`: [FIX] doc generation issue
* :ghpull:`2136`: [Fix]  laplacian_regularization on MAPMRI + cleanup warning
* :ghpull:`2140`: BF: Fix NumPy warning when creating arrays from ragged sequences
* :ghpull:`2139`: BF: Use equality check instead of identity check
* :ghpull:`2108`: [Horizon] Update clipping range on slicer
* :ghpull:`2121`: BF: ensure `btens` attribute of `GradientTable` is initialised
* :ghpull:`2129`: BF: Fix sequence stacking warning in LiFE tracking
* :ghpull:`2133`: BF: Fix NumPy warning when creating arrays from ragged sequences
* :ghpull:`2125`: ENH: function to calculate anisotropy of b-tensors
* :ghpull:`2124`: BUAN framework documentation
* :ghpull:`2033`: RF - Direction getters naming
* :ghpull:`2111`: Added an epsilon to bounding_box check
* :ghpull:`2086`: WIP Issue 1996
* :ghpull:`2091`: Modified the model for multiple hidden layers
* :ghpull:`2057`: DOC: Add DIPY dataset list to documentation.
* :ghpull:`2103`: Documentation typos, grammar corrections & imports
* :ghpull:`2088`: BUAN paper code and CLIs
* :ghpull:`2120`: rename var sp to sph
* :ghpull:`2113`: BF: refer to cigar_tensor
* :ghpull:`2116`: fixed code tags and minor changes
* :ghpull:`2100`: Fixed typos, grammatical errors and time import
* :ghpull:`2101`: Minor typos and imports
* :ghpull:`2095`: Fixed typos in dipy.align
* :ghpull:`2099`: Minor Typos and imports in the beginning
* :ghpull:`2102`: Modules imported in the beginning
* :ghpull:`2055`: Multidimensional gradient table
* :ghpull:`2097`: Replace manual sform values with get_best_affine
* :ghpull:`2104`: Fixed minor typos
* :ghpull:`2065`: Some typos and grammatical errors
* :ghpull:`2090`: Small fix reorient_bvecs
* :ghpull:`2067`: Some spelling and grammatical mistakes
* :ghpull:`2093`: Placed all imports in the beginning
* :ghpull:`2077`: Fixed minor typos in tutorials
* :ghpull:`2071`: Some change backs
* :ghpull:`2084`: Kunakl07 patch 7
* :ghpull:`2085`: Kunakl07 patch 8
* :ghpull:`2068`: Some spelling and grammatical errors
* :ghpull:`2069`: some typos
* :ghpull:`2063`: Gibbs tutorial patch
* :ghpull:`2045`: [Fix] workflow variable string
* :ghpull:`2060`: Replace old function with cython version
* :ghpull:`2058`: DOC: Fix `Sphinx` link in `CONTRIBUTING.md`
* :ghpull:`2059`: DOC: Add `Azure Pipelines` to CI tools in `CONTRIBUTING.md`
* :ghpull:`2056`: MAINT: Up Numpy version to 1.12.
* :ghpull:`2053`: Correct TYPO on the note about n_points in _gibbs_removal_2d()
* :ghpull:`2043`: [NF] Add a Deprecation system
* :ghpull:`2047`: [fix] Doc generation issue
* :ghpull:`2044`: [FIX] check seeds dtype
* :ghpull:`2041`: BF: SFM prediction with mask
* :ghpull:`2039`: Remove __future__
* :ghpull:`2042`: Add tests to rng module
* :ghpull:`2040`: RF: Swallow a couple of warnings that are safe to ignore.
* :ghpull:`2038`: [DOC] Update repo path
* :ghpull:`2037`: DOC: fix typo in FW DTI tutorial
* :ghpull:`2028`: Adapted for patch_radius with radii differing xyz direction.
* :ghpull:`2035`: DOC: Update DKI documentation according to the new get data functions

Issues (164):

* :ghissue:`2114`: Tutorial title in Streamline-based registration section is misleading
* :ghissue:`2207`: [FIX] Horizon shader warning
* :ghissue:`2208`: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13)
* :ghissue:`1793`: ENH: Improving Command Line and WF Docs
* :ghissue:`2007`: Reference for `load_trk` in recobundles example
* :ghissue:`2061`: Is dipy.viz supported in Colab or Kaggle Notebooks?
* :ghissue:`2070`: Python has stopped working during import
* :ghissue:`2107`: PNG images saved by window.record in the tutorial example are always black
* :ghissue:`2153`: lowercase .rst file names
* :ghissue:`2138`: Basic introduction to CLI needs better dataset to showcase capabilities
* :ghissue:`2194`: LiFE  model won't fit ?
* :ghissue:`2157`: BF: Fix variable may be used uninitialized warning
* :ghissue:`2177`: VIZ: streamline actor failing on Windows + macOS due to the new VTK9
* :ghissue:`2205`: Add optional installs for different settings.
* :ghissue:`2204`: from Renderer to scene
* :ghissue:`2183`: _streamlines_in_mask bounds check
* :ghissue:`2182`: `target_line_based` might read out of bounds
* :ghissue:`2203`: End of line period in sft
* :ghissue:`2200`: BF: Fix `'tp_print' is deprecated` Cython warning
* :ghissue:`2142`: ENH: function to calculate size/shape parameters of b-tensors and vice-versa
* :ghissue:`2199`: BUG: Fix NumPy and Cython deprecation and initialization warnings
* :ghissue:`2195`: [ENH] Validate streamlines pre-LiFE
* :ghissue:`2161`: Fix a memory overlap bug in multi_median (and median_otsu)
* :ghissue:`2163`: BF: Fix Cython label defined but not used warning
* :ghissue:`2174`: Improve performance of tissue classification
* :ghissue:`2168`: add fig_kwargs
* :ghissue:`2178`: Add full SH basis
* :ghissue:`2193`: BUAN_flow.rst to buan_flow.rst
* :ghissue:`2196`: [Fix] update save_vtk_streamlines and load_vtk_streamlines
* :ghissue:`2175`: Save streamlines as vtk polydata to a supported format file updated t…
* :ghissue:`2188`: [Fix] update mapmri due to cvxpy 1.1
* :ghissue:`2190`: Reconstruction with Multi-Shell Multi-Tissue CSD
* :ghissue:`2051`: BF: Non-negative Least Squares for IVIM
* :ghissue:`2176`: [DOC] Update SH basis documentation
* :ghissue:`2173`: Install ssl certificate for azure pipeline windows
* :ghissue:`2172`: fetch_gold_standard_io fetcher failed regularly
* :ghissue:`2169`: saving tracts in obj format
* :ghissue:`2170`: Output of utils.density_map() using tck file is different than MRTrix
* :ghissue:`2171`: Gitter url update: from nipy/dipy to dipy/dipy
* :ghissue:`2144`: Move gitter to dipy/dipy?
* :ghissue:`2154`: Bundle segmentation CLI tutorial
* :ghissue:`2162`: BF: Fix string literal comparison warning
* :ghissue:`2156`: BF: Fix Cython signed vs. unsigned integer comparison warning
* :ghissue:`2160`: TST: Change assert_equal(statement, True) to assert_(statement).
* :ghissue:`2158`: BF: Fix Cython floating point absolute value warning
* :ghissue:`2155`: [Fix] sfm RuntimeWarning
* :ghissue:`2159`: BF: Fix Cython different sign integer comparison warning
* :ghissue:`2147`: BF: Fix Cython function  override warning
* :ghissue:`2148`: BF: Fix `distutils` Python version requirement option warning
* :ghissue:`2151`: [DOC] Fixed minor typos, grammar errors and moved imports up in all examples
* :ghissue:`2130`: Checking empty Cluster objects generates NumPy warning
* :ghissue:`2131`: Elementwise comparison failure warning in multi_voxel test
* :ghissue:`2150`: [Fix] some warning on clustering test
* :ghissue:`2149`: [Fix] some warning on stats module
* :ghissue:`2145`: Rename dipy_track command line
* :ghissue:`2152`: changed buan_flow.rst to BUAN_flow.rst
* :ghissue:`2146`: Cluster threshold parameter in dipy_buan_shapes workflow
* :ghissue:`2128`: Registration Module failing with pre-matrix on Travis with future Numpy/Scipy release
* :ghissue:`2134`: Slicing, adding function of StatefulTractogram
* :ghissue:`2001`: Basic processing documentation for CLI.
* :ghissue:`2135`: [Fix] shm.py RuntimeWarning
* :ghissue:`2141`: [FIX] doc generation issue
* :ghissue:`2136`: [Fix]  laplacian_regularization on MAPMRI + cleanup warning
* :ghissue:`1765`: Refactor  dipy/stats/analysis.py
* :ghissue:`2122`: [WIP] Add build template
* :ghissue:`2140`: BF: Fix NumPy warning when creating arrays from ragged sequences
* :ghissue:`2139`: BF: Use equality check instead of identity check
* :ghissue:`2127`: DOC : Minor grammar fixes and moved imports up with respective comments
* :ghissue:`2108`: [Horizon] Update clipping range on slicer
* :ghissue:`2121`: BF: ensure `btens` attribute of `GradientTable` is initialised
* :ghissue:`2129`: BF: Fix sequence stacking warning in LiFE tracking
* :ghissue:`2133`: BF: Fix NumPy warning when creating arrays from ragged sequences
* :ghissue:`2125`: ENH: function to calculate anisotropy of b-tensors
* :ghissue:`2124`: BUAN framework documentation
* :ghissue:`2126`: dipy / fury fails to install on Ubuntu 18 with pip3
* :ghissue:`2033`: RF - Direction getters naming
* :ghissue:`2111`: Added an epsilon to bounding_box check
* :ghissue:`2112`: [WIP] BUndle ANalytics (BUAN) pipeline documentation
* :ghissue:`2086`: WIP Issue 1996
* :ghissue:`2091`: Modified the model for multiple hidden layers
* :ghissue:`2096`: Deep Code
* :ghissue:`2057`: DOC: Add DIPY dataset list to documentation.
* :ghissue:`2103`: Documentation typos, grammar corrections & imports
* :ghissue:`2088`: BUAN paper code and CLIs
* :ghissue:`2120`: rename var sp to sph
* :ghissue:`2118`: Local namespace of Scipy is same as a variable name
* :ghissue:`1861`: WIP: Refactoring the stats module
* :ghissue:`2113`: BF: refer to cigar_tensor
* :ghissue:`2116`: fixed code tags and minor changes
* :ghissue:`2024`: DIPY open lab meetings, Winter 2020
* :ghissue:`2100`: Fixed typos, grammatical errors and time import
* :ghissue:`2101`: Minor typos and imports
* :ghissue:`2094`: Detailed Beginner Friendly Tutorials
* :ghissue:`2095`: Fixed typos in dipy.align
* :ghissue:`2099`: Minor Typos and imports in the beginning
* :ghissue:`2102`: Modules imported in the beginning
* :ghissue:`2055`: Multidimensional gradient table
* :ghissue:`2097`: Replace manual sform values with get_best_affine
* :ghissue:`2105`: Tutorial Symmetric Regn 3D patch 3
* :ghissue:`2104`: Fixed minor typos
* :ghissue:`2078`: Applying affine transform to streamlines in a SFT object
* :ghissue:`2065`: Some typos and grammatical errors
* :ghissue:`1305`: Questions/policies about writing .rst/web doc files
* :ghissue:`2090`: Small fix reorient_bvecs
* :ghissue:`2067`: Some spelling and grammatical mistakes
* :ghissue:`2093`: Placed all imports in the beginning
* :ghissue:`2077`: Fixed minor typos in tutorials
* :ghissue:`2089`: Transforming bvecs after registration
* :ghissue:`2071`: Some change backs
* :ghissue:`2084`: Kunakl07 patch 7
* :ghissue:`2085`: Kunakl07 patch 8
* :ghissue:`2072`: Some typos and grammatical errors in faq.rst
* :ghissue:`2073`: Some minor grammatical fixes old_highlights.txt
* :ghissue:`2074`: Small typos
* :ghissue:`2075`: Some grammatical changes in maintainer_workflow.rst
* :ghissue:`2076`: Some grammatical changes in maintainer_workflow.rst
* :ghissue:`2079`: Some minor typos in gimbal_lock.rst
* :ghissue:`2080`: Some minor grammatical errors fixes
* :ghissue:`2081`: Some typos and grammatical corrections in Changelog
* :ghissue:`2082`: Grammatical fixes in readme.rst
* :ghissue:`2083`: Fixes in regtools.py
* :ghissue:`2066`: Fixed some typos
* :ghissue:`2068`: Some spelling and grammatical errors
* :ghissue:`2069`: some typos
* :ghissue:`2063`: Gibbs tutorial patch
* :ghissue:`2045`: [Fix] workflow variable string
* :ghissue:`2060`: Replace old function with cython version
* :ghissue:`2058`: DOC: Fix `Sphinx` link in `CONTRIBUTING.md`
* :ghissue:`2059`: DOC: Add `Azure Pipelines` to CI tools in `CONTRIBUTING.md`
* :ghissue:`1363`: MDF not working properly
* :ghissue:`2056`: MAINT: Up Numpy version to 1.12.
* :ghissue:`1871`: apply transformation to all volumes in a series of DWI (4D)
* :ghissue:`2052`: dipy.tracking.utils.density_map order of arguments changed by mistake
* :ghissue:`1785`: Could we use gifti for streamlines?
* :ghissue:`1728`: Bug in shm_coeff computation?
* :ghissue:`1699`: Details in aparc-reduced.nii.gz
* :ghissue:`1671`: Question about shm_coeff
* :ghissue:`1552`: dti.py - quantize_evecs - error
* :ghissue:`1373`: How to convert from converted isotropic to original resolution (anisotropic)
* :ghissue:`1364`: SNR estimation troubleshooting
* :ghissue:`1152`: nan gfa and odf values when mask includes voxels with 0 dwi signal
* :ghissue:`1047`: Gradient flipped in the x-direction - FSL bvecs handling
* :ghissue:`2019`: Apply deformation map to render "registered" image
* :ghissue:`2049`: KFA calculation
* :ghissue:`2048`: Group analysis
* :ghissue:`2053`: Correct TYPO on the note about n_points in _gibbs_removal_2d()
* :ghissue:`2043`: [NF] Add a Deprecation system
* :ghissue:`218`: Callable response broken in csd module
* :ghissue:`2047`: [fix] Doc generation issue
* :ghissue:`313`: csdeconv response as callable
* :ghissue:`1848`: Add Dipy to MRI-Hub (ISMRM Reproducible Research Study Group)
* :ghissue:`2044`: [FIX] check seeds dtype
* :ghissue:`2034`: Using the tutorial on Euler method on my data
* :ghissue:`2041`: BF: SFM prediction with mask
* :ghissue:`1724`: Failure on Windows/Python 3.5
* :ghissue:`1938`: Auto-clearing the AppVeyor queue backlog
* :ghissue:`2039`: Remove __future__
* :ghissue:`2042`: Add tests to rng module
* :ghissue:`1864`: Add tests to dipy.core.rng
* :ghissue:`2040`: RF: Swallow a couple of warnings that are safe to ignore.
* :ghissue:`2038`: [DOC] Update repo path
* :ghissue:`2037`: DOC: fix typo in FW DTI tutorial
* :ghissue:`2028`: Adapted for patch_radius with radii differing xyz direction.
* :ghissue:`2035`: DOC: Update DKI documentation according to the new get data functions

DIPY 1.1.1

----------

- 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 MTMS 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.