Skip to content

Version 0.5
Compare
Choose a tag to compare
@36000 36000 released this 13 Oct 22:38
· 2003 commits to master since this release
0.5
c826d64

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)
Assets 2
Loading