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@arokem arokem released this 05 Jan 14:48
· 1707 commits to master since this release
0.6
e1a58f4

This version includes many fixes, documentation enhancements and
performance optimizations. It also drops Python 3.6 support.
This version matches our first paper describing/using the software.

  • Add more timing information (#622)
  • Allow CLI to specify what api method is called (#623)
  • Plot tweaks to make paper quality (#576)
  • Reduce apm test workload (#621)
  • Split up nightly 5 (#620)
  • Fix test_AFQ_init, may allow nightly 3 to pass (#619)
  • Dilate the ROIs. (#618)
  • Enh Add Callosum ROIs support (#538)
  • BF: Need to read these parameters from file, before getting the data. (#615)
  • Drop Python 3.6 support. (#612)
  • BF: use get instead of get_nearest (#610)
  • [ENH] [DOC] Add matlab to python file conversion functions, add docs for custom tractography integration (#599)
  • [FIX] calculate sl counts on the spot (#605)
  • DOC: Example that explores BIDS and includes tractography from another pipeline. (#577)
  • Allow more flexible definition of endpoint filtering atlas. (#589)
  • DOC: Explain that trk files are saved in RASMM. (#604)
  • Removes several unused CLIs. (#588)
  • BF: Use the provided x and y inputs. (#606)
  • [ENH] added reco80 example (#567)
  • [DOC]Add mask.rst file to give context and explanation to masks (#598)
  • Reuse the CSD sh coefficients if you already have them. (#591)
  • [ENH] Allow the user to specify what range the color by volume should shade over (#594)
  • Adding dummy end points for custom bundles (#543)
  • [ENH] Allow user to optionally normalize density map maximum values to 1 (#595)
  • [ENH] Add cloudknot example (#533)
  • [ENH] Robust tensor fitting (#580)
  • FIX: Traverse BIDS hierarchy to find masks, bvals, and bvecs (#587)
  • NF: Adds DKI AWF to scalars. (#592)
  • Read and resample ROI data. (#545)
  • DOC: Adds some documentation for developers of the software. (#546)
  • initialize for subject and session pairs where dwi files exist (#583)
  • [FIX] Put tg in rasmm first for SLR registration (#566)
  • [FIX] Unflip Plotly x axis; multiple flexibility improvements in plotly plotting for paper (#581)
  • WIP DEP: Bump numpy version (#579)
  • adding nb_streamlines to segmentation parameters (#570)
  • [ENH] add weighted option for dice (#568)
  • Adds prealign stage to the examples. (#555)
  • Eliminate force_recompute option. (#552)
  • Warn when templateflow creates directory (#557)
  • 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)
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