Releases · PennLINC/qsirecon

This is a prerelease for the version that will be used by the HBCD project for their first data release.

We plan to not introduce any backwards-incompatible changes for a while.

What's Changed

🛠 Breaking Changes

Rename QSIPrep to QSIRecon by @tsalo in #1
Start removing QSIPrep-specific code and documentation by @tsalo in #4
Remove QSIPrep-specific parameters and Config elements by @tsalo in #6
Drop Docker wrapper by @tsalo in #52
Restructure outputs into BIDS datasets by @tsalo in #66
Combine mfp and mdp entities into single param entity by @tsalo in #72
Replace --recon-input-pipeline with --input-type by @tsalo in #68
Remove unused --longitudinal argument by @tsalo in #88
Make all params and models lower-case by @tsalo in #90
Reorganize atlas management based on XCP-D and BIDS-Atlas by @tsalo in #123
Rename --freesurfer-input to --fs-subjects-dir by @tsalo in #152
[ENH] Read session-specific anat data by @mattcieslak in #151
Remove underscore versions of all parameters by @tsalo in #159
Make connectivity field names compatible with MATLAB by @tsalo in #166

🎉 Exciting New Features

Add ng, perng, parng, and mapcoeffs to Dipy MAPMRI outputs by @tsalo in #55
Add DatasetLinks to dataset_description.json by @tsalo in #77
Pass DWI file metadata to reconstruction workflows by @tsalo in #154
Add HBCD Release1 recon workflow by @mattcieslak in #169

🐛 Bug Fixes

Write out QSIRecon pipeline-wise reports by @tsalo in #7
Write out reports to individual reconstruction derivative folders by @tsalo in #53
Add summary reportlets to HTML report by @tsalo in #61
Fix QSIRecon Entrypoint by @smeisler in #76
Use file lock to avoid concurrent edits to dataset_description.json by @cookpa in #91
Compress the tck files by @tsalo in #93
Add missing filename patterns by @tsalo in #131
Fix infant anatomical ingression by @tsalo in #126
Fix extension in ds_fs_5tt_hsvs by @tsalo in #165
Fix extension in ds_qsiprep_5tt_hsvs by @tsalo in #172
Fix space in ds_qsiprep_5tt_hsvs by @tsalo in #175
Make PlotPeaks robust enough that we don't need --writable-tempfs in singularity/apptainer by @mattcieslak in #174

Other Changes

Remove internal version of LiterateWorkflow by @tsalo in #8
Drop and modify infrastructure files by @tsalo in #40
Remove QSIPrep-specific tests by @tsalo in #5
Drop unused modules, classes, and functions by @tsalo in #11
[CI] Speed up pyafq test by @mattcieslak in #57
[DOCS] Reorganize documentation by @mattcieslak in #56
Collect templates from TemplateFlow instead of package data by @tsalo in #49
Remove unused data files by @tsalo in #63
Replace hyperlinks with BibTeX references by @tsalo in #67
[DOCS] Add scalar tables by @mattcieslak in #80
Move scalar file configs to YAMLs and use a recon scalar workflow by @tsalo in #79
[WIP] Make a system for keeping docs and file names in sync by @mattcieslak in #86
Convert pipeline configs from JSON to YAML by @tsalo in #84
[DOCS] clean up by @mattcieslak in #101
Draft pre-init ingression by @tsalo in #102
[ENH] Update AMICO by @mattcieslak in #115
[FIX] mif2fib by @ameliecr in #116
Fix how bundles to be tracked are selected for DSIstudio autotrack by @ameliecr in #121
[FIX] workflow connection in dsi_studio_gqi by @mattcieslak in #142
[CI] add hsvs test by @mattcieslak in #136
[FIX] dsi_studio_gqi workflow connect by @mattcieslak in #146
[DOC] Minor addition for skipping connectivity matrices step by @chiuhoward in #150
Add page documenting output structure by @tsalo in #156
Add information about QSIPrep/QSIRecon releases by @tsalo in #158
[CI] Add tests for reading pre-1.0 outputs from qsiprep by @mattcieslak in #155
[ENH] Support outputs from qsiprep 1.0.0rc0 by @mattcieslak in #160
[FIX] get rid of logging error #145 by @mattcieslak in #161
Add UKB ingression by @smeisler in #147
[FIX] set TMPDIR before running plot_peaks by @mattcieslak in #163
[ENH] match to qsiprep nipype/nireports versions by @mattcieslak in #167
Add in Val's text for connectivity matrices by @mattcieslak in #173
Disable test_main in the CI integration tests by @mattcieslak in #177