1.4.1

A minor release for a major issue fixed when using scil_validate_bids with phase and mag data.

Thank you @EmmaRenauld @frheault @AlexVCaron 🎉

What's Changed

• Creating module 'labels' by @EmmaRenauld in #648
• [ENH] POC : Use mocking to get faster execution of tests by @AlexVCaron in #639
• Unit tests for the new labels module by @frheault in #659
• --no_empty in scil_remove invalid streamlines.py by @frheault in #657
• [ENH][BF] scil_validate_bids by @arnaudbore in #661
• [BF] Bids validate by @arnaudbore in #663

Full Changelog: 1.4.0...1.4.1

1.4.0

Holy 🐮 🐮 🐮 !

🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀
🚀 Congrats everybody for this amazing work ! 🚀
🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀

SCILUS team you rock !! 🎉

🔥 @CHrlS98 🔥
🔥 @EmmaRenauld 🔥
🔥 @AlexVCaron 🔥
🔥 @karanphil 🔥
🔥 @frheault 🔥
🔥 @AntoineTheb 🔥

What's Changed

• Better docstring for scil_validate_and_correct_bvecs by @CHrlS98 in #570
• Improve DOC on scil_resample_tractogram.py by @frheault in #574
• Fix wrong condition for is_voxel_in_bound used in dev tracking by @CHrlS98 in #569
• Small fixes and improvements in tractogram filtering scripts by @EmmaRenauld in #567
• Adding new filtering script by orientation by @EmmaRenauld in #571
• Fix fix dsi studio by @frheault in #572
• Add mask option for bingham fit and metrics by @CHrlS98 in #573
• Fixing coordinate type + decreasing test size in dev tracking by @EmmaRenauld in #581
• Warn user for rk > 1 with prob tracking in dev tracking by @CHrlS98 in #580
• Clean pep8 in the fetcher file by @EmmaRenauld in #582
• Modifying scil_score tractogram by @EmmaRenauld in #568
• Simple GPU tracking by @CHrlS98 in #576
• Small changes in the dev tracker by @EmmaRenauld in #585
• Fixing transform_anatomy by @karanphil in #586
• Add split image script by @karanphil in #584
• Enhance GPU tracking by @CHrlS98 in #587
• Upgrading dipy by @EmmaRenauld in #578
• Fix case with no wpc in scil_score_tractogram by @EmmaRenauld in #595
• Modify scil_cut_streamlines.py by @karanphil in #588
• [BF] Fix arg in invalid streamlines + warning in todi by @arnaudbore in #589
• [BF] Fix bug in scil_concatenate_dwi.py when supplying more than 2 images by @CHrlS98 in #603
• Fix lazy usage with tck files by @EmmaRenauld in #598
• Fix F1 score by @EmmaRenauld in #600
• ENH: Add overlapping volume mosaic screenshot script by @jhlegarreta in #577
• ENH: Adding QBx option in subsampling + cleaning by @EmmaRenauld in #590
• Clarify vox space by @EmmaRenauld in #593
• Update prepare eddy by @arnaudbore in #609
• update jenkins and requirements by @arnaudbore in #611
• ENH: scil scoring unique streamlines by @AntoineTheb in #614
• Added a 'must_pass_mask' by @EmmaRenauld in #599
• [BF] Update bundle metrics - handle NaN by @arnaudbore in #619
• New assign color options by @frheault in #566
• Add a function to verify compatibility by @arnaudbore in #616
• Moving methods by @EmmaRenauld in #621
• New method to get n seeds at once. by @EmmaRenauld in #597
• Add arguments for RGB color ODF and RGB background color by @karanphil in #612
• Change default interpolation for mask by @CHrlS98 in #625
• Fix jenkins by @arnaudbore in #635
• [WIP] Correlate dwi QC by @frheault in #528
• WIP: New labels maps and simplification of tractometry profile scripts by @frheault in #554
• [ENH] Add multiple ID to filter tractogram with atlas by @arnaudbore in #627
• scil_assign_custom_color_to_tractogram.py optional colorbar image output by @CHrlS98 in #629
• Trilinear interpolation + sf threshold for GPU tracking by @CHrlS98 in #613
• ENH: unit test PoC by @AntoineTheb in #631
• Creating new script to score tractogram that is already segmented. by @EmmaRenauld in #622
• Bug fix for scil_swap_gradient_axis by @CHrlS98 in #634
• [ENH] Validate bids by @arnaudbore in #591
• Fix rare division by 0 in f1 by @EmmaRenauld in #642
• Gradient sampling ajustment by @karanphil in #626
• [ENH] Extract gradient scheme from eddy output - for tractoflow by @arnaudbore in #623
• Tensor format by @EmmaRenauld in #637
• [BF] validate BIDS by @arnaudbore in #645
• Fix: names for overreach by @EmmaRenauld in #643
• Add check_bbox_false (only in scil_score_bundles) by @EmmaRenauld in #646
• Fix logging across scilpy by @frheault in #647
• Fix logging for RBx (file handling) by @frheault in #649
• Fix total count by @EmmaRenauld in #650
• [BF] BG color as optional function argument by @CHrlS98 in #651
• Fix fetcher by @EmmaRenauld in #655
• BF validate_bids when full reverse by @arnaudbore in #654

Full Changelog: 1.3.0...1.4.0

1.4.0-rc4

Last rc before release !

What's Changed

• Fix total count by @EmmaRenauld in #650
• [BF] BG color as optional function argument by @CHrlS98 in #651
• Fix fetcher by @EmmaRenauld in #655
• BF validate_bids when full reverse by @arnaudbore in #654

Full Changelog: 1.4.0-rc3...1.4.0-rc4

1.4.0-rc3

Fix for RBX_flow

What's Changed

• Fix logging for RBx (file handling) by @frheault in #649

Full Changelog: 1.4.0-rc2...1.4.0-rc3

1.4.0-rc2

Second release candidate

Almost there !

What's Changed

• Fix logging across scilpy by @frheault in #647

Full Changelog: 1.3.0...1.4.0-rc2

1.4.0-rc1

A lot of thing have been done. Thank you !!!! 🥳

What's Changed

• Better docstring for scil_validate_and_correct_bvecs by @CHrlS98 in #570
• Improve DOC on scil_resample_tractogram.py by @frheault in #574
• Fix wrong condition for is_voxel_in_bound used in dev tracking by @CHrlS98 in #569
• Small fixes and improvements in tractogram filtering scripts by @EmmaRenauld in #567
• Adding new filtering script by orientation by @EmmaRenauld in #571
• Fix fix dsi studio by @frheault in #572
• Add mask option for bingham fit and metrics by @CHrlS98 in #573
• Fixing coordinate type + decreasing test size in dev tracking by @EmmaRenauld in #581
• Warn user for rk > 1 with prob tracking in dev tracking by @CHrlS98 in #580
• Clean pep8 in the fetcher file by @EmmaRenauld in #582
• Modifying scil_score tractogram by @EmmaRenauld in #568
• Simple GPU tracking by @CHrlS98 in #576
• Small changes in the dev tracker by @EmmaRenauld in #585
• Fixing transform_anatomy by @karanphil in #586
• Add split image script by @karanphil in #584
• Enhance GPU tracking by @CHrlS98 in #587
• Upgrading dipy by @EmmaRenauld in #578
• Fix case with no wpc in scil_score_tractogram by @EmmaRenauld in #595
• Modify scil_cut_streamlines.py by @karanphil in #588
• [BF] Fix arg in invalid streamlines + warning in todi by @arnaudbore in #589
• [BF] Fix bug in scil_concatenate_dwi.py when supplying more than 2 images by @CHrlS98 in #603
• Fix lazy usage with tck files by @EmmaRenauld in #598
• Fix F1 score by @EmmaRenauld in #600
• ENH: Add overlapping volume mosaic screenshot script by @jhlegarreta in #577
• ENH: Adding QBx option in subsampling + cleaning by @EmmaRenauld in #590
• Clarify vox space by @EmmaRenauld in #593
• Update prepare eddy by @arnaudbore in #609
• update jenkins and requirements by @arnaudbore in #611
• ENH: scil scoring unique streamlines by @AntoineTheb in #614
• Added a 'must_pass_mask' by @EmmaRenauld in #599
• [BF] Update bundle metrics - handle NaN by @arnaudbore in #619
• New assign color options by @frheault in #566
• Add a function to verify compatibility by @arnaudbore in #616
• Moving methods by @EmmaRenauld in #621
• New method to get n seeds at once. by @EmmaRenauld in #597
• Add arguments for RGB color ODF and RGB background color by @karanphil in #612
• Change default interpolation for mask by @CHrlS98 in #625
• Fix jenkins by @arnaudbore in #635
• [WIP] Correlate dwi QC by @frheault in #528
• WIP: New labels maps and simplification of tractometry profile scripts by @frheault in #554
• [ENH] Add multiple ID to filter tractogram with atlas by @arnaudbore in #627
• scil_assign_custom_color_to_tractogram.py optional colorbar image output by @CHrlS98 in #629
• Trilinear interpolation + sf threshold for GPU tracking by @CHrlS98 in #613
• ENH: unit test PoC by @AntoineTheb in #631
• Creating new script to score tractogram that is already segmented. by @EmmaRenauld in #622
• Bug fix for scil_swap_gradient_axis by @CHrlS98 in #634
• [ENH] Validate bids by @arnaudbore in #591
• Fix rare division by 0 in f1 by @EmmaRenauld in #642
• Gradient sampling ajustment by @karanphil in #626
• [ENH] Extract gradient scheme from eddy output - for tractoflow by @arnaudbore in #623
• Tensor format by @EmmaRenauld in #637
• [BF] validate BIDS by @arnaudbore in #645
• Fix: names for overreach by @EmmaRenauld in #643
• Add check_bbox_false (only in scil_score_bundles) by @EmmaRenauld in #646

Full Changelog: 1.3.0...1.4.0-rc1

1.3.0

After almost a month of testing the day has come.

Welcome scilpy 1.3.0 - less buggy 🐛 and RISHer 😄

First contribution from @grahamlittlephd. Congrats !

What's Changed

• BF: apply transfo tractogram when no streamlines by @arnaudbore in #523
• Improve code style in (bitbucket-imported) tracking files by @EmmaRenauld in #508
• Powder avg by @grahamlittlephd in #524
• ENH: Return data in original space when transforming streamlines by @jhlegarreta in #526
• ENH: Remove unused default process count parameter by @jhlegarreta in #530
• Modifications in the (bitbucket) tracking scripts - part 2 by @EmmaRenauld in #511
• Update processing.zip checksum by @CHrlS98 in #534
• BF: save trk when no keep invalid by @arnaudbore in #535
• BF: visualise bundles mosaic when no streamlines by @arnaudbore in #539
• Fixel-based lobe-specific metrics from bundle by @CHrlS98 in #527
• Optional uniformize by @frheault in #529
• Update test data for processing and tracking by @CHrlS98 in #540
• Compute RISH features from SH image by @ppoulin91 in #538
• Estimate bundle diameter by @frheault in #499
• Tracking part3 by @EmmaRenauld in #532
• compute_connectivity fix average by @frheault in #541
• Asymmetric tracking unlocked for dev tracking scripts by @CHrlS98 in #544
• fix_transform_warp_dtype by @frheault in #547
• fix_left_out_voxel in apply_bias_field_on_dwi by @frheault in #548
• Angle-aware filtering with optional GPU acceleration by @CHrlS98 in #525
• Add option to scale SF by the b0 in scil_compute_sf_from_sh.py by @ppoulin91 in #545
• change api to download gdrive by @arnaudbore in #550
• Bump pillow from 8.3.2 to 9.0.0 by @dependabot in #536
• Bump pillow from 8.3.2 to 9.0.0 in /docs by @dependabot in #537
• Adding a cut streamlines tools by @frheault in #542
• Bug fix: Multi-tissue fODF convergence error by @CHrlS98 in #551
• remove mmap option by @arnaudbore in #549
• Update to numpy 1.21.* by @arnaudbore in #552
• Fix bundle_adjacency docstring (voxel) by @frheault in #553
• [BF] Remove exception for non-symmetric sphere for dev tracking by @CHrlS98 in #556
• Fixing doc in io.utils by @EmmaRenauld in #557
• [BF] Prepare Eddy - Index creation by @arnaudbore in #558
• Fix vf stuff by @karanphil in #559
• Bump pillow from 9.0.0 to 9.0.1 in /docs by @dependabot in #562
• Bump pillow from 9.0.0 to 9.0.1 by @dependabot in #563
• Adding count display in scil_outlier_rejection by @EmmaRenauld in #561
• Fix scil visualize histogram add resolution assert by @grahamlittlephd in #565

New Contributors

• @grahamlittlephd made their first contribution in #524

Full Changelog: 1.2.2...1.3.0

1.3.0-rc2

A couple of 🐛 fixed before releasing.

[BF] Eddy @arnaudbore
[BF] Remove exception for non-symmetric sphere for dev tracking @CHrlS98

Improve docstring (@EmmaRenauld @karanphil )

1.3.0-rc1

First release candidate for 1.3.0.

Here are few new features:

• RISH features from SH image
• Fixel-based lobe-specific metrics from bundle
• New structure for tracking
• Angle-aware filtering with optional GPU acceleration
• Estimate bundle diameter
• Cut streamlines tools

Some 🐛 fixed:

• Save trk when no keep invalid
• Visualise bundles mosaic when no streamlines
• Apply transfo tractogram when no streamlines
• Multi-tissue fODF convergence error

Thank you to all of you especially @CHrlS98 @GuillaumeTh @frheault @ppoulin91 @EmmaRenauld @jhlegarreta

1.2.2

A brand new release with a lot of new features/scripts and a little bit less buggy.

New scripts:

• scil_compute_qball_metrics.py
• scil_resample_tractogram.py
• scil_group_comparison.py

New feature:

• Add inverse operation flag - transformation tractograms
• Compute asymmetric TODI + specific metrics
• Support empty bundle in tractometry

Bugs fixed 🐛 :

• Streamlines math
• Volume reslice
• BIDS validation

A huge thank you to @CHrlS98 @GuillaumeTh @AntoineTheb @frheault and @jhlegarreta for you contributions.