2.1.1

Minor modification for a new release 🎉

• Fix scil_bundle_label_map.py
• New BundleParc v2

What's Changed

• ENH: BundleParc v2 by @AntoineTheb in #1179
• ENH: shorten scil_fodf_bundleparc.py --help by @AntoineTheb in #1189
• ENH: Add miscellaneous tractogram extensions to header check by @jhlegarreta in #1191
• Test energy_comparison by @karanphil in #1190
• NF - Region-Adaptive Propagation (RAP) tractography by @gabknight in #1192
• [BF] Improve scil_bundle_label_map add filtering by @arnaudbore in #1197
• Update version + typo by @arnaudbore in #1198

Full Changelog: 2.1.0...2.1.1

2.1.0

Release 2.1.0

It's here, it's shiny and it comes with a ton of new features 🎉 and less bugs 🐛 .
Don't hesitate to take a look at the API.

Thank you everybody !

What's Changed

• Tractogram scripts parts4 by @EmmaRenauld in #961
• Tractogram scripts part 5 by @EmmaRenauld in #983
• Tractogram scripts part6 by @EmmaRenauld in #991
• Tractogram scripts part7: segmentation scripts by @EmmaRenauld in #993
• [FIX] 10 colors in BASE10 colors for visualization by @AlexVCaron in #999
• [FIX] Empty remaining indices when filtering for a bundle by @levje in #1002
• Removing xform from convert script by @frheault in #1001
• Generate HDF5 from TRKs by @frheault in #985
• [FIX] Typo in scil_dti_metrics script by @AlexVCaron in #1000
• Update COMMIT AMICO - use args.processes by @arnaudbore in #998
• ENH: tractogram add dps by @AntoineTheb in #1006
• Update to work with Trimeshpy 0.0.4 by @frheault in #1003
• ENH: rework scil_tractogram_cut_streamlines + scil_labels_from_mask by @AntoineTheb in #1009
• Add create surface by @arnaudbore in #1005
• [FIX] Missing parameter for background viz by @levje in #1012
• [ENH] Add script normalize bvec by @arnaudbore in #1011
• [BF] Fix surfaces lib by @arnaudbore in #1014
• [ENH] Bundle fixel analysis script by @karanphil in #1004
• Removing unused argument in scil_bundle_fixel_analysis.py by @karanphil in #1018
• Alter tractogram (trim, cut, replace, subsample, transform) by @frheault in #992
• Modify lesions_info to support labels instead of mask by @frheault in #1020
• New script to compute similarity between mask and atlas (nii) by @frheault in #994
• [ENH] Uniformize surface apply transformation by @arnaudbore in #1015
• Distance map by @frheault in #1023
• Fix tests by @arnaudbore in #1028
• Tractograms: more unit tests by @EmmaRenauld in #1027
• ENH: Pad or crop volume using scil_volume_reshape.py by @AntoineTheb in #1019
• WIP "Fake" ambiant occlusion for MI-Brain by @frheault in #1030
• Nawm generation based on distance map by @frheault in #1026
• return option min_vol_lesion by @ThoumyreStanislas in #1036
• [BF] Fix save FODF add header info from i_dwi by @arnaudbore in #1037
• ENH: cut streamlines min length by @AntoineTheb in #1040
• [ENH][BF] Update json conversion to excel used in tractometry_flow by @arnaudbore in #1041
• [FIX] pyproject.toml and right build dependencies. by @levje in #1048
• Denoise nl_means script by @EmmaRenauld in #972
• Scilpy bot v2 by @frheault in #1033
• ENH: better bundle endpoints maps by @AntoineTheb in #1047
• Add no norm option to scil_bundle_fixel_analysis by @karanphil in #1032
• [ENH] Add mrds scripts part 3 by @arnaudbore in #1046
• Keep old space by @frheault in #1050
• [ENH] Add mrds scripts part 1 by @arnaudbore in #1021
• [ENH] Add mrds scripts part 2 by @arnaudbore in #1022
• FIX: ratio arg in volume pairwise comparison by @AntoineTheb in #1051
• Fibertube Tracking by @VincentBeaud in #971
• Connectivity: compute_matrices script by @EmmaRenauld in #1031
• Improve coverage in multiprocessing cases by @EmmaRenauld in #1053
• Fix doc by @EmmaRenauld in #1056
• [ENH] Fix resample local_tracking_dev accepts close iso voxels by @arnaudbore in #1055
• [ENH] Add precision to FRF scripts by @AlexVCaron in #1057
• Create new script compute_simple_matrix by @EmmaRenauld in #1045
• ENH: add interpolation to scil_volume_apply_transform by @AntoineTheb in #1065
• [BF] Tractogram filter by multiples ROIs - Crash by @arnaudbore in #1052
• Add Fibertube_tracking.rst to the read-the-docs by @CHrlS98 in #1070
• Fibertube tracking - New endpoint scoring by @VincentBeaud in #1064
• New Endpoint Scoring - Charles' suggestions by @VincentBeaud in #1075
• Script dps math by @VincentBeaud in #1066
• Add test single shell NODDI by @karanphil in #1080
• Adding ref to scil_freewater_maps by @karanphil in #1083
• Clarify doc to differentiate dpp_math with dps mode and dps_math by @VincentBeaud in #1081
• Avoid scalar with dim > 0 by squeezing. Passes test and pep8 no warning. by @VincentBeaud in #1078
• Fix merge queue by @AlexVCaron in #1109
• Tracking local custom seeds by @VincentBeaud in #1069
• [FIX]: Return rejected streamlines with empty sft by @levje in #1076
• [DOC] Add documentation for grid_intersections by @CHrlS98 in #1079
• Switch to loops simple connectivity by @frheault in #1082
• FIX: Filter streamlines by length, use the "save rejection" argument. by @levje in #1090
• Fix the hdf5 error when dpp are present by @gagnonanthony in #1092
• Fix Fury upcoming deprecation call by @AlexVCaron in #1085
• BF for asymmetric peaks by @CHrlS98 in #1077
• Move plot residuals into viz - plot by @zinelya in #1088
• Fixing bug in gradients_generate_sampling by @karanphil in #1094
• DOC - fixed updated script name by @gabknight in #1107
• Next connectivity scripts by @EmmaRenauld in #1063
• FIX: Division by 0 in scil_dti_metrics by @AntoineTheb in #1089
• Update script scil_viz_gradients_screenshot by @karanphil in #1097
• Condense distance matrix that was not. Pep8 + test pass by @VincentBeaud in #1084
• Cleaning the connectivity pairwise agreement script by @EmmaRenauld in #1087
• update to dipy 1.10 by @arnaudbore in #1114
• Fixing the skip_b0_check function by @karanphil in #1113
• Cythonization warnings by @CHrlS98 in #1101
• [BF] NODDI map catch error by @arnaudbore in #1115
• [ENH] Allow extra option for topup and eddy by @arnaudbore in #1117
• Adding support for list of lists of paths in assert_inputs_exist by @karanphil in #1086
• Final connectivity scripts PR by @EmmaRenauld in #1099
• Small fix (issue 1123) by @EmmaRenauld in #1126
• Support .tck for commit by @EmmaRenauld in #1125
• RF - Input to volume stats scripts by @gabknight in #1068
• Add script to validate gradient tables by @karanphil in #1110
• Fibertube Density by @VincentBeaud in #1112
• Add Scilpy version - part 1 by @zinelya in #1100
• Add Scilpy version - part 2 by @zinelya in #1106
• BF - fixed voxel bundary conditions in uncompress streamlines by @gabknight in #1098
• Delete script fix_trk by @EmmaRenauld in #984
• [ENH] Add positionnal arguments by @arnaudbore in #1118
• DOC - renamed the uncompress fct to streamlines_to_voxel_coordinates by @gabknight in #1103
• bids_validate func get_data -> changed clean: Boolean definition from… by @Desk3505 in https://gi...

2.1.0rc1

New scilpy release coming up

First release candidate - published on pypi

2.2.0-rc1

New SCILPY release coming !

Before jumping into the real release with are starting with a rc1 pre release. 🎉
A lot have been done and we'll get into the details when we'll reach the 2.2.0 release

Thank you to all our contributors !

SCILPY Team

What's Changed

• Tractogram scripts parts4 by @EmmaRenauld in #961
• Tractogram scripts part 5 by @EmmaRenauld in #983
• Tractogram scripts part6 by @EmmaRenauld in #991
• Tractogram scripts part7: segmentation scripts by @EmmaRenauld in #993
• [FIX] 10 colors in BASE10 colors for visualization by @AlexVCaron in #999
• [FIX] Empty remaining indices when filtering for a bundle by @levje in #1002
• Removing xform from convert script by @frheault in #1001
• Generate HDF5 from TRKs by @frheault in #985
• [FIX] Typo in scil_dti_metrics script by @AlexVCaron in #1000
• Update COMMIT AMICO - use args.processes by @arnaudbore in #998
• ENH: tractogram add dps by @AntoineTheb in #1006
• Update to work with Trimeshpy 0.0.4 by @frheault in #1003
• ENH: rework scil_tractogram_cut_streamlines + scil_labels_from_mask by @AntoineTheb in #1009
• Add create surface by @arnaudbore in #1005
• [FIX] Missing parameter for background viz by @levje in #1012
• [ENH] Add script normalize bvec by @arnaudbore in #1011
• [BF] Fix surfaces lib by @arnaudbore in #1014
• [ENH] Bundle fixel analysis script by @karanphil in #1004
• Removing unused argument in scil_bundle_fixel_analysis.py by @karanphil in #1018
• Alter tractogram (trim, cut, replace, subsample, transform) by @frheault in #992
• Modify lesions_info to support labels instead of mask by @frheault in #1020
• New script to compute similarity between mask and atlas (nii) by @frheault in #994
• [ENH] Uniformize surface apply transformation by @arnaudbore in #1015
• Distance map by @frheault in #1023
• Fix tests by @arnaudbore in #1028
• Tractograms: more unit tests by @EmmaRenauld in #1027
• ENH: Pad or crop volume using scil_volume_reshape.py by @AntoineTheb in #1019
• WIP "Fake" ambiant occlusion for MI-Brain by @frheault in #1030
• Nawm generation based on distance map by @frheault in #1026
• return option min_vol_lesion by @ThoumyreStanislas in #1036
• [BF] Fix save FODF add header info from i_dwi by @arnaudbore in #1037
• ENH: cut streamlines min length by @AntoineTheb in #1040
• [ENH][BF] Update json conversion to excel used in tractometry_flow by @arnaudbore in #1041
• [FIX] pyproject.toml and right build dependencies. by @levje in #1048
• Denoise nl_means script by @EmmaRenauld in #972
• Scilpy bot v2 by @frheault in #1033
• ENH: better bundle endpoints maps by @AntoineTheb in #1047
• Add no norm option to scil_bundle_fixel_analysis by @karanphil in #1032
• [ENH] Add mrds scripts part 3 by @arnaudbore in #1046
• Keep old space by @frheault in #1050
• [ENH] Add mrds scripts part 1 by @arnaudbore in #1021
• [ENH] Add mrds scripts part 2 by @arnaudbore in #1022
• FIX: ratio arg in volume pairwise comparison by @AntoineTheb in #1051
• Fibertube Tracking by @VincentBeaud in #971
• Connectivity: compute_matrices script by @EmmaRenauld in #1031
• Improve coverage in multiprocessing cases by @EmmaRenauld in #1053
• Fix doc by @EmmaRenauld in #1056
• [ENH] Fix resample local_tracking_dev accepts close iso voxels by @arnaudbore in #1055
• [ENH] Add precision to FRF scripts by @AlexVCaron in #1057
• Create new script compute_simple_matrix by @EmmaRenauld in #1045
• ENH: add interpolation to scil_volume_apply_transform by @AntoineTheb in #1065
• [BF] Tractogram filter by multiples ROIs - Crash by @arnaudbore in #1052
• Add Fibertube_tracking.rst to the read-the-docs by @CHrlS98 in #1070
• Fibertube tracking - New endpoint scoring by @VincentBeaud in #1064
• New Endpoint Scoring - Charles' suggestions by @VincentBeaud in #1075
• Script dps math by @VincentBeaud in #1066
• Add test single shell NODDI by @karanphil in #1080
• Adding ref to scil_freewater_maps by @karanphil in #1083
• Clarify doc to differentiate dpp_math with dps mode and dps_math by @VincentBeaud in #1081
• Avoid scalar with dim > 0 by squeezing. Passes test and pep8 no warning. by @VincentBeaud in #1078
• Fix merge queue by @AlexVCaron in #1109
• Tracking local custom seeds by @VincentBeaud in #1069
• [FIX]: Return rejected streamlines with empty sft by @levje in #1076
• [DOC] Add documentation for grid_intersections by @CHrlS98 in #1079
• Switch to loops simple connectivity by @frheault in #1082
• FIX: Filter streamlines by length, use the "save rejection" argument. by @levje in #1090
• Fix the hdf5 error when dpp are present by @gagnonanthony in #1092
• Fix Fury upcoming deprecation call by @AlexVCaron in #1085
• BF for asymmetric peaks by @CHrlS98 in #1077
• Move plot residuals into viz - plot by @zinelya in #1088
• Fixing bug in gradients_generate_sampling by @karanphil in #1094
• DOC - fixed updated script name by @gabknight in #1107
• Next connectivity scripts by @EmmaRenauld in #1063
• FIX: Division by 0 in scil_dti_metrics by @AntoineTheb in #1089
• Update script scil_viz_gradients_screenshot by @karanphil in #1097
• Condense distance matrix that was not. Pep8 + test pass by @VincentBeaud in #1084
• Cleaning the connectivity pairwise agreement script by @EmmaRenauld in #1087
• update to dipy 1.10 by @arnaudbore in #1114
• Fixing the skip_b0_check function by @karanphil in #1113
• Cythonization warnings by @CHrlS98 in #1101
• [BF] NODDI map catch error by @arnaudbore in #1115
• [ENH] Allow extra option for topup and eddy by @arnaudbore in #1117
• Adding support for list of lists of paths in assert_inputs_exist by @karanphil in #1086
• Final connectivity scripts PR by @EmmaRenauld in #1099
• Small fix (issue 1123) by @EmmaRenauld in #1126
• Support .tck for commit by @EmmaRenauld in #1125
• RF - Input to volume stats scripts by @gabknight in #1068
• Add script to validate gradient tables by @karanphil in #1110
• Fibertube Density by @VincentBeaud in #1112
• Add Scilpy version - part 1 by @zinelya in #1100
• Add Scilpy version - part 2 by @zinelya in #1106
• BF - fixed voxel bundary conditions in uncompress streamlines by @gabknight in #1098
• Delete script fix_trk by @EmmaRenauld in #984
• [ENH] Add positionnal arguments by @arnaudbore in #1118
• DOC - renamed the uncompress fct to streamlines_to_voxel_coordinates by @gabknight in #1103
• bids_validate func get_data -> changed clean: Boolean definiti...

2.0.2

SCILPY release 2.0.2 🎉

I didn't think I'd be back here so quickly.
Again a couple of issues have been fixed .

See you soon—I hope it's not too soon, though.

What's Changed

• [FIX] fixed typo in surface convert script by @grahamlittlephd in #989
• [BF] Fix mask type - dwi apply bias field by @arnaudbore in #990

Full Changelog: 2.0.1...2.0.2

2.0.1

SCILPY release 2.0.1 🎉

I told you 😂
A couple of issues have been fixed and it makes scilpy even better than before. 💯
See you soon 😉

What's Changed

• Easy tests reconst by @EmmaRenauld in #982
• Fix verifications in volume_resample by @EmmaRenauld in #986
• Add param sub_sphere to tracking_local_dev by @arnaudbore in #987
• Volumes test by @EmmaRenauld in #942
• Fix wrong import in legacy file by @EmmaRenauld in #988

Full Changelog: 2.0.0...2.0.1

2.0.0

⚠️ New SCILPY release 2.0.0 ⚠️

This is huge step for scilpy and our community !

This is a major refactoring of the code.
All our scripts are now organized into categories, I encourage you to check the new documentation https://scilpy.readthedocs.io/en/latest/
As always a lot of new features, unit tests and bug fixes.

Thank you to our new contributors ! 🎉
BIG thank you to all contributors especially @EmmaRenauld , @karanphil , @CHrlS98 , @AlexVCaron 🥳

See you soon 😉

What's Changed

• Volumes modules by @EmmaRenauld in #747
• Streamline operations tests by @EmmaRenauld in #762
• Create a assert_roi_radii_format function for FRF scripts by @karanphil in #771
• Connectomics module by @EmmaRenauld in #764
• Removing frf_table option by @karanphil in #772
• Move load img by @karanphil in #775
• Noddi clean up by @mdesco in #770
• Dti clean up by @mdesco in #773
• Module Gradient by @EmmaRenauld in #779
• add mti.py in reconst by @Manonedde in #768
• Asym clean up by @mdesco in #776
• fodf cleanup, deleted obselete and more by @mdesco in #788
• DWI module by @mdesco in #781
• Modify mti by @Manonedde in #786
• Support multiple input to merge (for PR in connectoflow) by @frheault in #761
• RF - changed tracking default sphere from symmetric724 to repulsion724 by @gabknight in #769
• Adding volume operations tests by @gagnonanthony in #783
• [BF] fix trk space when filter by length by @arnaudbore in #796
• Gradient sampling refactor, part2 by @EmmaRenauld in #790
• FIX: bug in scil_score_bundles.py by @AntoineTheb in #798
• [ENH] Add fix trk startrack by @arnaudbore in #797
• Fix flip startrack by @arnaudbore in #800
• Move bvec_bval_tool from utils to gradients module by @EmmaRenauld in #799
• Add test volume_math by @frheault in #778
• scil_convert_fdf.py by @arnaudbore in #801
• ENH: Adding option to skip randomization of seed. + other fixes by @EmmaRenauld in #757
• Simple framework to port scripts into legacy by @AlexVCaron in #807
• scil_merge_json move function into module by @arnaudbore in #803
• adding vtk legacy options to scil_convert_surface script by @ThoumyreStanislas in #795
• FIX/ENH: Streamline (and mask) operations refactor by @AntoineTheb in #774
• Final check main of script 1) dwi 2) gradient by @EmmaRenauld in #802
• ENH: Add Parallel Transport Tractography to scil_compute_local_tracking by @AntoineTheb in #750
• Cleaning reconst module by @karanphil in #806
• Fix round_bvals_to_shell by @karanphil in #811
• Move valid inputs from reorder_philips into module gradients by @arnaudbore in #787
• BF - metadata version when using editable install by @gabknight in #812
• Fixing scil_visualize_bundles_mosaic.py with Pillow 10.0.* by @karanphil in #814
• RF - Tracking/Tractogram Scripts by @gabknight in #815
• Legacy installation by @arnaudbore in #824
• Rename labels scripts and deprecate old by @EmmaRenauld in #819
• Rename dwi scripts by @karanphil in #823
• [Fix] Change wrong help description by @EmmaRenauld in #825
• ENH: refactor scil_compute_local_tracking by @AntoineTheb in #813
• FIX: scil_cut_streamlines now properly handles loops by @AntoineTheb in #817
• Rename connectomics and deprecate old by @EmmaRenauld in #820
• FIX import new main by @EmmaRenauld in #832
• Rename volume scripts by @arnaudbore in #829
• Rename surface scripts by @arnaudbore in #827
• Rename reconst scripts by @karanphil in #822
• Add legacy test (help) by @EmmaRenauld in #833
• Rename convert scripts by @arnaudbore in #828
• Rename reorder_dwi by @arnaudbore in #835
• Rename gradients scripts by @karanphil in #834
• [FIX] Use numbers rather than letters in scil_gradients_modify_axes by @EmmaRenauld in #821
• RF - Tractogram Scripts Renaming by @gabknight in #837
• Moving OP out of the default output files from scil_btensor_metrics.py. by @karanphil in #836
• General testing for all legacy scripts by @gabknight in #838
• Rename tractometry by @EmmaRenauld in #842
• Rename denoising by @EmmaRenauld in #847
• fix_surface_renaming by @frheault in #849
• Add throttling to jenkins pipeline by @AlexVCaron in #851
• TST - remove legacy warnings by @gabknight in #848
• RF - Scripts Renaming by @gabknight in #856
• Adding tolerance argument to fodf msmt by @karanphil in #839
• Rename some tractogram scripts by @EmmaRenauld in #846
• Rename scripts by @arnaudbore in #845
• DOC - tracking by @gabknight in #861
• [WIP] Add_verbose_arg by @ThoumyreStanislas in #850
• [WIP] Add_version_scilpy by @ThoumyreStanislas in #868
• [ENH] Add coverage by @arnaudbore in #869
• Rename small utils by @EmmaRenauld in #852
• Improved docstring and renaming by @frheault in #857
• Rename "lobe-specific metrics" to "Bingham metrics" by @CHrlS98 in #863
• Add multiple fs folder subject possibility by @arnaudbore in #844
• ENH: merge gradients convert by @AntoineTheb in #854
• Merge asymmetric filtering scripts by @CHrlS98 in #855
• Update help prompts to fit new name + add formerly: line for old script name. by @gagnonanthony in #860
• Fix basename compute dwi snr by @Manonedde in #873
• Update doc surface by @grahamlittlephd in #864
• [BF] tractoflow filter by roi by @arnaudbore in #876
• [ENH] Add pull request template by @arnaudbore in #875
• Update to dipy 1.8 by @arnaudbore in #853
• fix gdrive endpoint for tests by @AlexVCaron in #877
• Update memsmt fodf script [requires dipy 1.8.0] by @karanphil in #791
• OPT - map sh to sf before tracking [requires dipy 1.8.0] by @gabknight in #782
• Fix the script for unequal bval by @frheault in #881
• rename some scripts by @arnaudbore in #878
• Bump pillow from 10.0.1 to 10.2.0 by @dependabot in #882
• Bump pillow from 10.0.1 to 10.2.0 in /docs by @dependabot in #883
• add step to publish coverage to codecov.io by @AlexVCaron in #886
• Add Otsu threshold to scil_volume_math.py by @CHrlS98 in #887
• Fix bad commit in codecov by @AlexVCaron in #888
• Robustify the coloring by @EmmaRenauld in #890
• [WIP] Kill Jenkins by @AlexVCaron in #892
• Cancel previous concurrent build by @AlexVCaron in #893
• run workflow on PR head by @AlexVCaron in #897
• pass fetcher to DVC by @AlexVCaron in #895
• FIX: scil_visualize_connectivity text rotation by @AntoineTheb in #894
• Add perpendicular diffusi...

1.7.0-dev

This is a temporary pre-release used only for dev purposes.

---

YOU SHOULD NOT BE USING THIS VERSION -

---

1.6.0

New SCILPY release 1.6.0

First of all congrats to @EliseCos for her first PR 🎉 !!

A lot of new features and bug fixes. Thanks to @EmmaRenauld @CHrlS98 @karanphil @AlexVCaron @frheault !!

Good job everybody !

What's Changed

• [BF] Error message - metrics stats in ROI by @arnaudbore in #702
• [BF] GPU tracking kernel cannot be called main by @CHrlS98 in #701
• Get version script by @frheault in #703
• Adding import matplotlib to assign_custom_color_to_tractogram by @karanphil in #713
• Upgrade dipy to 1.7.0 by @CHrlS98 in #712
• Adding options for normalization in scil_assign_custom_color_to_tractogram by @karanphil in #717
• Adding absolute_peak_values to scil_compute_fodf_metrics.py by @karanphil in #715
• Fix: Add bundle to scores if it was not found by @EmmaRenauld in #709
• Refactor asym_odf_metrics script by @CHrlS98 in #708
• Add angle coloring option + fix bugs by @EmmaRenauld in #718
• Adding legacy options to scil_convert_sh_basis.py by @karanphil in #704
• [ENH] Add soft distance for each filter by @arnaudbore in #719
• Correlation ops by @frheault in #721
• (WIP) Harmonize json by @frheault in #716
• [ENH] Add new parameter to overwrite filter distance by @arnaudbore in #723
• Fix permissions by @frheault in #726
• Upgrade filter overwrite distance - Add criteria by @arnaudbore in #727
• RBx with FSS by @frheault in #707
• Multi centro labels map by @frheault in #728
• BUG: Allow tractogram math script to run as such by @jhlegarreta in #729
• Optional out_indices in scil_extract_dwi_shells.py by @CHrlS98 in #724
• Display masks as contours in screenshots by @AlexVCaron in #705
• ENH: Verbose tracking by @EmmaRenauld in #714
• Fix validate BIDS by @arnaudbore in #710
• Correct ihMTsat by @karanphil in #732
• Make stopping criteria more obvious + more similar to dipy. by @EmmaRenauld in #699
• Unit test tractogram operations by @EmmaRenauld in #706
• Sphere subdivide by @EliseCos in #731
• Working Scilpy development container for VS Code by @AlexVCaron in #733
• Fix filter anatomically by @arnaudbore in #735
• Fix bug with new .gitattributes by @AlexVCaron in #737
• Update citation for RBx -> BundleSeg by @frheault in #738
• Module streamline operations by @EmmaRenauld in #736
• Fix undetected bug after modifying module tractogram. by @EmmaRenauld in #739
• Add rejected streamlines to scil_filter_tractogram_anatomically by @arnaudbore in #740
• Remove pairwise by @frheault in #744
• Fix a few warnings by @EmmaRenauld in #748
• Use hot dipy 1.8.0.dev0 by @arnaudbore in #749
• Custom ROI surface rendering for Laurent by @frheault in #746
• Fix interp surf rendering by @frheault in #753
• Bump pillow from 9.0.1 to 10.0.1 in /docs by @dependabot in #755
• Bump pillow from 9.0.1 to 10.0.1 by @dependabot in #756
• ENH: scil_tractogram_math support for TCKs by @AntoineTheb in #752
• Merge gpu tracking into scil_compute_local_tracking.py by @CHrlS98 in #743
• Update version and README by @arnaudbore in #759

New Contributors

• @EliseCos made their first contribution in #731

Full Changelog: 1.5.0...1.6.0

1.5.0

NEW RELEASE 🎉 🥳

A lot of things have changed since the last version.
Thank you to every single one of you for contributing to scilpy.

What's Changed

• Testing 3 10 upgrade by @frheault in #662
• Fixing unique in dev branch by @frheault in #668
• Python3 10 readme by @frheault in #666
• [ENH] scilpy and python3.10 by @arnaudbore in #678
• Parallelise remove_loops_and_sharp_turns by @arnaudbore in #677
• Change version number by @frheault in #681
• Project streamlines from/to wm/gm by @frheault in #640
• Coloring connectomics by @frheault in #636
• Added OLO to reorder_connectivity by @frheault in #630
• New script: Plot dipy sphere by @EmmaRenauld in #679
• Fix multiprocess in dev tracking by @EmmaRenauld in #676
• Add python3.10-venv to packages to install by @CHrlS98 in #682
• skip init in search_keyword. by @frheault in #683
• Fixing uniform_coloring in scil_visualize_bunldes.py by @karanphil in #672
• Reactivate md5sum in fetcher by @frheault in #684
• uint8 in compute_density when possible by @frheault in #685
• Fix validate bids by @arnaudbore in #674
• Switch to kdtree for uniformize --target by @frheault in #686
• Adding variance to scil_visualize_fodf by @karanphil in #671
• Add check_bbox argument management by @EmmaRenauld in #641
• Adding PCA script for dimension reduction of metrics by @gagnonanthony in #673
• Module tractogram operations by @EmmaRenauld in #658
• fix seed mask empty by @arnaudbore in #687
• Adding small_dims option to scil_compute_fodf_max_in_ventricles by @karanphil in #688
• Adding explanations to scil_compute_fodf_max_in_ventricles by @karanphil in #689
• Fix some deprecated import and fix some tests by @arnaudbore in #690
• Fixing warning always showing up. by @EmmaRenauld in #693
• Fix default sphere tracking by @arnaudbore in #692
• Update to hotdipy + fix load empty sft by @arnaudbore in #694
• [WIP] Adding b-tensor encoding scripts like compute_fodf/frf and metrics by @karanphil in #425
• [ENH] Upload frozen python requirements aside of release assets by @AlexVCaron in #695
• (WIP) Adding script to apply transform to bvecs by @karanphil in #696
• Fix warnings in distortion correction by @arnaudbore in #700

New Contributors

• @gagnonanthony made their first contribution in #673

Full Changelog: 1.4.2...1.5.0