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)