Scilpy

Last rc before release !

What's Changed
* Fix total count by EmmaRenauld in https://github.com/scilus/scilpy/pull/650
* [BF] BG color as optional function argument by CHrlS98 in https://github.com/scilus/scilpy/pull/651
* Fix fetcher by EmmaRenauld in https://github.com/scilus/scilpy/pull/655
* BF validate_bids when full reverse by arnaudbore in https://github.com/scilus/scilpy/pull/654


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.4.0-rc3...1.4.0-rc4

Fix for RBX_flow

What's Changed
* Fix logging for RBx (file handling) by frheault in https://github.com/scilus/scilpy/pull/649


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.4.0-rc2...1.4.0-rc3

Second release candidate

Almost there !

What's Changed
* Fix logging across scilpy by frheault in https://github.com/scilus/scilpy/pull/647

**Full Changelog**: https://github.com/scilus/scilpy/compare/1.3.0...1.4.0-rc2

A lot of thing have been done. Thank you !!!! :partying_face:

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


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.3.0...1.4.0-rc1

After almost a month of testing the day has come.

Welcome scilpy 1.3.0 - less buggy :bug: and RISHer :smile:

First contribution from grahamlittlephd. Congrats !

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

New Contributors
* grahamlittlephd made their first contribution in https://github.com/scilus/scilpy/pull/524

**Full Changelog**: https://github.com/scilus/scilpy/compare/1.2.2...1.3.0

A couple of :bug: fixed before releasing.

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

Improve docstring (EmmaRenauld karanphil )