Version 0.4

0.4 (August 17, 2020)

This release adds several new registration templates and techniques, providing
major improvements in bundle segmentation with waypoint ROIs. In addition, new
visualization methods using plotly were introduced, to generate HTML-based
visualizations of bundles, and to compare longitudinal measurements. This version
relies on pybids for parsing of input datasets. Many other bug fixes and improvements.

• Throw error when backend is misnamed (#363)
• Export what is natural to the viz library (#361)
• Upgrade FURY to support newer VTK (#359)
• Allow for selecting subject(s) by position after randomization (#352)
• Ignore positional arguments in non AFQ functions for docstring parser, add test (#354)
• Auto doc fix (#350)
• Clips streamlines by the inclusion ROI. (#159)
• S3 Bids Fetch Fixes (#340)
• BF: AFQ derivatives should be saved inside "derivatives/afq" (#348)
• Compare profiles from CSVs (#317)
• New CLI / Config (#310)
• Update versions of scipy and vtk. (#342)
• Generating a wm mask out of multiple scalars (#330)
• Add classes for fetching a BIDS-compliant study on S3 (#290)
• Remove this section of the pyproject. (#337)
• Setup with config redux ... redux (#326)
• Updates DIPY url used in metadata. (#333)
• b0_threshold default updated (#331)
• Make power maps the default for registration (#329)
• b value selection fix and test, power map test, models moved to own submodule (#322)
• Revert "Adds a setup.cfg file and cleans up metadata and other hacks" (#324)
• Adds a setup.cfg file and cleans up metadata and other hacks (#320)
• Allow user to customize registration targets, fix some other aspects of registration (#283)
• Bvals preallocation (#63)
• Remove hcc from defaults (#315)
• export_all function (#312)
• Kaleido instead of orcas (#311)
• Viz module uses fury and plotly (#289)
• Allow study selection for fetch_hcp (#300)
• RF: Speed up testing by moving viz test into API run. (#302)
• Pybids (#284)
• Plot tract profiles in CLI (#280)
• Remove cloukdnot examples (#297)
• Make save intermediates folder if it does not already exist (#296)
• Remove six (#295)
• use rapidfuzz instead of fuzzywuzzy (#266)
• Extra requirements feature added, consistent with current requirement files (#291)
• Bump pybids to 0.11.1 (#293)
• make_bundle_dict should only be called after reg_template is settled (#281)
• Add instructions for disabling github actions on forked repos. (#287)
• Fix two bugs, makes tests work (#282)
• Visualize all tract profiles for a scalar in one plot (#268)
• Profile format changed to be less tall and more wide, like mAFQ (#279)
• Added random_seed parameter in tractography (#270)
• Bring fetch_hcp into alignment with other fetch functions (#272)
• Api File Naming (#269)
• Fixed numpydoc version to 0.9.2 (#271)
• Use xvfb_wrapper for aws (#257)
• Save mask as float32, so that we can open it in MI-Brain. (#260)
• Update reqs 253 (#254)
• Use valid value for Zenodo license field. (#249)
• BF: Use Tableau 20 colors for the 20 waypoint-defined bundles. (#251)
• BF: Actually use the user-provided path for saving HCP files. (#250)

Version 0.3

This release includes several important fixes and enhancements. In particular, a significant bug in prealignment of the template to individual data is now fixed in #232. Additional accuracy of alignment is also provided by registering to a skull-stripped template provided through templateflow. Several new features include a new class for fiber groups and bundles and animated visualizations of results that are provided as a standard part of the CLI pipeline.

• NF: Add dki to api (#238, JK)
• DOC: Fixes error in installation instructions (#244, AR)
• NF: Add fiber group class (#184, JK)
• RF: Read the MNI template from templateflow, instead of DIPY. (#224, AR)
• NF: Adds a flag to save intermediate variables within Segmentation (#237, AR)
• NF: Integrate the bundle gif viz into the CLI. (#242, AR)
• NF: Automatically infer sh_order (#240, AR)
• NF: Update bundle visualization and add export gif to API (#229, JK)
• BF: Fix warping (#232, AN)
• BF: More API Fixes (#228, JK)
• BF: Restore force recompute (#225, AR)

Version 0.2

0.2 (February 20, 2020)

This release introduces some changes to the main API module, to incorporate all
helper functions into the API class. This should not affect user API.

• RF: Api Usability (#207; JK)

Version 0.1.2

0.1.2 (February 14, 2020)

This release fixes a bug in the way that indices of streamlines are handled,
introduce a Boutiques descriptor and includes other small fixes for automation.

• NF: CLI fixes and creation of a Boutiques descriptor (#206; GK)
• NF: Usage tracking with popylar (#205; AR)
• BF: clean_by_endpoints should be able to return the indices. (#204; AR)
• DOC: Adds an example of downloading some example data and organizing it. (#211)
• MAINT: Use only the setuptools_scm version string. Removing all others. (#199; AR)
• MAINT: Use setuptools_scm to add the git hash to the version string. (#198; AR)
• MAINT: Maintenance tools (#222; AR)

Version 0.1.1

Version 0.1.1