This release allow users to provide custom tractography and registration templates using pyBIDS filters. We added the new tractography method PFT/ACT and the new reconstruction method MSMT. RecoBundles can now use the Yeh 80 bundle atlas. Many minor bug fixes and enhancements.
- Save non anat positioned bundles in their own plots (#539)
- Allow bundle dict as input to afq object (#540)
- Put msmt in nightly 3 (#542)
- Actually use MSMT in API call (#530)
- Update test_init to additional df columns; add nightly 5 test yml (#531)
- NIGHTLY: move reco80 to 4; break up nightly 3 to isolate bug (#525)
- Multi-shell, multi-tissue model (#474)
- BF: Reset the input tractogram space to what you originally got. (#520)
- FIX: Remove xvfb from being needed in tests (#522)
- FIX: Reco80 fixes (#503)
- FIX: specify that the b val range is inclusive (#523)
- ENH #443 Callosal Group Example (#476)
- adding separate example output directories to avoid name collisions (#490)
- FIX: Plotly viz bug fixes, and update to custom bundles (#513)
- FIX: Update all b0_thresholds to 50 (#507)
- FIX: update reg_subject arg checking to include dicts (#515)
- FIX: updates docstring in clean_bundle which returns sft, not nib.streamlines (#514)
- Try plotly as default, re-organize usage documentation (#439)
- FIX: Update tractography max_length docstring to be consistent (#508)
- Split off nightly 4 from nightly 3, nightly rests run python 3.8 (#501)
- ENH: Sort the bundles list from csv alphabetically in group csv comparison (#499)
- ENH Disabling progress bars for sphinx-gallery (#492)
- ENH: Dice coeff (#484)
- enh adding distclean and realclean targets for sphinx build (#489)
- FIX: Downsample number of streamlines vizzed down to 200 when vizzing all bundles (#482)
- ENH: Return contast index dataframe from contrast_index (#483)
- Require dipy versions higher than 0.12, so that we can use current ma… (#488)
- Reg algo automatically chosen based on whether mapping is provided, syn mapping for sls fixed, recobundle defaults updated (#472)
- Apply brain mask to subject img before registration (#478)
- FIX: export registered b0 should use inverse pre align to read mapping file (#479)
- Fix typos in api.afq type checking (#477)
- Type check AFQ object inputs (#456)
- Allow reg subject to be bids filters; refactor getting stanford data into temp folder (#458)
- Removes extraneous underscore. (#475)
- Adds total number of streamlines, to complete the sl counts table. (#469)
- Follow up on #462, to fix failing nightly test. (#470)
- FIX: remove whole brain from bundle list for sl count when using recobundles (#471)
- Fixes the timing table (#467)
- Updating pyAFQ documentation (#455)
- Streamline counts table (#468)
- Adjusting group comparison figures (#466)
- Adds 80-bundle atlas for RB (#431)
- Catch no subject error early (#463)
- Colorful legend when using cbv (#465)
- Give the APM map a more BIDS-ish name, and generate metadata file. (#462)
- FIX: Validate bids_path exists (#459)
- Give users the option to disable individual subject lines in plot (#446)
- Add PFT Mask. (#444)
- Rename profile columns back to standard column names (#445)
- Update plots to paper Quality (#429)
- Remove whole brain from bundle dict for reco viz (#438)
- Allow option to upload combined profile (#437)
- Add packaging requirement (#436)
- Allow user to input custom tractography (#422)
- Automatically choose bundle names for recobundles (#420)
- Skip nightly test that may be causing OOM (#428)
This micro release provides testing for Python 3.8 and multiple other fixes. This release requires the newly-released DIPY 1.2.0
- BF: Register the PVE to the parameters. (#423)
- Python 3.8 (#360)
- Further subdivide nightly tests (#419)
- Many minor bug fixes (#409)
- Divide nightly test into 2; have nightly tests only do nightly tests (#417)
- Raise error earlier for empty ROI (#415)
- Update example to serve as a CI target (#380)
- Convert local_directories set to list (#414)
- Update to Dipy 1.2.0 (#384)
- Adds ParticleFilteringTractography. (#335)
- A few visualization updates (#390)
- Timing dict name mismatch bug fix (#395)
- make decision to combine profile automatic in export_all (#387)
- Export timing information (#393)
- Remove unnecessary check (#389)
- Add ability to remove edges of profiles (#386)
- Add upload_to_s3, download_and_combine_afq_profiles (#376)
- Change nighty tests to happen at midnight, PST (#383)
- Use get_fdata instead of deprecated get_data in example (#377)
- Skip seg faulting test (#378)
- Overhaul Mask File UI; Other minor UI improvements (#370)
- Return a unique set of subjects in S3BIDSStudy._all_subjects (#373)
- Allow user to seed tractography with ROIs via api. Use this to reduce test times. Mark some tests as nightly. (#364)
- Added test that runs full cli pipeline on default config file. Tell CI to not run the tests marked slow. (#356)
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)
This release includes several important fixes and enhancements. In particular, prealignment of the template . Additional accuracy of alignment is provided by registering to a skull-stripped template provided through templateflow. A new class for fiber groups and bundles was introduced and animated visualizations of results 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)
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)
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)