# 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 `tools/github_stats.py`):

Pull Requests (60):

- PR #3095: [UPCOMING] Release preparation for 1.9.0

- PR #3086: [RF] Fix spherical harmonic terminology swap

- PR #3105: [doc] improve some tutorials rendering

- PR #3109: [BF] convert_tractogram fix

- PR #3108: enabled trx support with correct header

- PR #3107: enabled trx support for viz

- PR #3033: [RF] fix dki mask for nlls

- PR #3104: Dkimaskfix

- PR #3106: volume slices visibility fixed

- PR #3102: Bugfix for peaks slices and synchronization.

- PR #3078: return S0 from dki fit

- PR #3101: [BF] Uniformize cython version

- PR #3097: Feature/surface

- PR #3048: [TEST] Adds support of cython for pytest

- PR #3053: [NF] Add workflow to convert tensors in different formats

- PR #3073: [NF] Add DSI workflow

- PR #3099: [DOC] fix some typo [ci skip]

- PR #3098: Removing tensorflow addon from DL models

- PR #2973: Tab names for slice tabs as file names.

- PR #3081: NF: Adding N4 bias correction deep learning model

- PR #3092: Feature: volume synchronizing

- PR #3059: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors

- PR #3090: RF - changed memory view to double* trilinear_interpolation_4d

- PR #3080: Adding SH basis legacy option support to peaks_from_model

- PR #3087: backward compatibility fixed

- PR #3088: [TEST] Pin pytest

- PR #3084: fixed 4d slice issue

- PR #3083: Np.unique check removed.

- PR #3082: Add Fedora installation instructions [ci skip]

- PR #3076: [CI] Update scientific-python/upload-nightly-action to 0.5.0

- PR #3070: [DOC] Fix installation link in README [ci skip]

- PR #3069: [DOC] Fix DTI Tutorial [ci skip]

- PR #3063: [RF] remove cpdef in PmfGen

- PR #3054: [DOC] Fix some links [ci skip]

- PR #3060: Bump codecov/codecov-action from 3 to 4

- PR #3061: [OPT] Enable openmp for macOS wheel and CI’s

- PR #3049: [MTN] code cleaning: remove some dependencies version checking

- PR #3050: [RF] Move `dipy.boots.resampling` to `dipy.stats.resampling`

- PR #3051: [RF] Remove dipy.io.bvectxt module

- PR #3052: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874

- PR #3045: [DOC] fix multi_shell_fiber_response docstring array dims [ci skip]

- PR #3041: [NF] Add convert tractograms flow

- PR #3040: [BW] Remove some python2 reference

- PR #3039: [TEST] Add setup_module and teardown_module

- PR #3038: [NF] Update dipy_info: allow tractogram files format

- PR #3043: d/d/t/test_data.py: endian independent dtype.

- PR #3042: pyproject.toml: no cython at run time.

- PR #3027: [NF] Add Concatenate tracks workflows

- PR #3008: NF: add SH basis conversion between dipy and mrtrix3

- PR #3025: [TEST] Manage http errors for stateful tractograms

- PR #3031: Bugfix: Horizon image’s dtype validation

- PR #3021: [MTN] Remove 3.8 Ci’s

- PR #3026: [RF] Fix cython 3 warnings

- PR #3022: [DOC] Fix logo size and link [ci skip]

- PR #3013: Added Fibonacci spiral and test for it

- PR #3019: DOC: Fix link to toolchain roadmap page in README

- PR #3012: DOC: Document observance for Scientific Python min supported versions

- PR #3018: Bump actions/download-artifact from 3 to 4

- PR #3017: Bump actions/upload-artifact from 3 to 4

- PR #3014: Update release1.8.rst

Issues (81):

- #2970: spherical harmonic degree/order terminology swapped

- #3105: [doc] improve some tutorials rendering

- #3109: [BF] convert_tractogram fix

- #3108: enabled trx support with correct header

- #3107: enabled trx support for viz

- #2994: DKI masking

- #3033: [RF] fix dki mask for nlls

- #3104: Dkimaskfix

- #3106: volume slices visibility fixed

- #3102: Bugfix for peaks slices and synchronization.

- #2281: Black Output for pam5 file with dipy_horizon

- #3078: return S0 from dki fit

- #3101: [BF] Uniformize cython version

- #3097: Feature/surface

- #2719: pytest and cdef functions

- #3048: [TEST] Adds support of cython for pytest

- #3053: [NF] Add workflow to convert tensors in different formats

- #3073: [NF] Add DSI workflow

- #3099: [DOC] fix some typo [ci skip]

- #3098: Removing tensorflow addon from DL models

- #2973: Tab names for slice tabs as file names.

- #3081: NF: Adding N4 bias correction deep learning model

- #3092: Feature: volume synchronizing

- #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

- #3059: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors

- #3090: RF - changed memory view to double* trilinear_interpolation_4d

- #3080: Adding SH basis legacy option support to peaks_from_model

- #3085: Viz Tests failing

- #3087: backward compatibility fixed

- #3088: [TEST] Pin pytest

- #3074: Horizon for large datasets - concerns regarding np.unique

- #3075: Horizon - 4D data support - slicing on the 4-th dim

- #3084: fixed 4d slice issue

- #3083: Np.unique check removed.

- #3082: Add Fedora installation instructions [ci skip]

- #3065: Add s390x test workflow

- #3076: [CI] Update scientific-python/upload-nightly-action to 0.5.0

- #3070: [DOC] Fix installation link in README [ci skip]

- #3069: [DOC] Fix DTI Tutorial [ci skip]

- #3066: Dipy website incorrect image

- #3063: [RF] remove cpdef in PmfGen

- #3054: [DOC] Fix some links [ci skip]

- #3060: Bump codecov/codecov-action from 3 to 4

- #3061: [OPT] Enable openmp for macOS wheel and CI’s

- #3057: Using the atlas HCP1065 in DIPY

- #3055: [RF] replace Bunch by Enum

- #3049: [MTN] code cleaning: remove some dependencies version checking

- #3050: [RF] Move `dipy.boots.resampling` to `dipy.stats.resampling`

- #3051: [RF] Remove dipy.io.bvectxt module

- #3052: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874

- #2789: Horizon image’s dtype validation

- #3047: “Editable” installation broken

- #3045: [DOC] fix multi_shell_fiber_response docstring array dims [ci skip]

- #3041: [NF] Add convert tractograms flow

- #3040: [BW] Remove some python2 reference

- #3039: [TEST] Add setup_module and teardown_module

- #3038: [NF] Update dipy_info: allow tractogram files format

- #3043: d/d/t/test_data.py: endian independent dtype.

- #3042: pyproject.toml: no cython at run time.

- #3027: [NF] Add Concatenate tracks workflows

- #3035: If I want to use 6D array in “actor.odf_slicer”, how can i do?

- #2993: Add conversion utility between DIPY and MRtrix3 spherical harmonic basis

- #3008: NF: add SH basis conversion between dipy and mrtrix3

- #3025: [TEST] Manage http errors for stateful tractograms

- #3031: Bugfix: Horizon image’s dtype validation

- #3032: Consider moving your nightly wheel away from the scipy-wheel-nightly (old location) to scientific-python-nightly-wheels

- #3021: [MTN] Remove 3.8 Ci’s

- #3003: DIPY installation raises Cython warnings

- #3026: [RF] Fix cython 3 warnings

- #2852: Different behavior regarding color channels of horizon

- #2378: A novice’s request for advice on loading very large tractograms (.tck)

- #2064: How to register MR to CT of the same person?

- #2601: read_bvals_bvecs can’t read double volume dwi

- #3022: [DOC] Fix logo size and link [ci skip]

- #3013: Added Fibonacci spiral and test for it

- #3020: load_nifti import doesn’t work if using submodule directly

- #3019: DOC: Fix link to toolchain roadmap page in README

- #3012: DOC: Document observance for Scientific Python min supported versions

- #3018: Bump actions/download-artifact from 3 to 4

- #3017: Bump actions/upload-artifact from 3 to 4

- #3014: Update release1.8.rst

- #1525: Clang-omp moved to boneyard on brew