What’s New

1.1.0

πŸŽ‰ Exciting New Features

  • Tissue fraction modulated ICVF and OD maps by @araikes in https://github.com/PennLINC/qsirecon/pull/218

  • Calculate kurtosis microstructure scalars with new DKI_reconstruction parameter by @tsalo in https://github.com/PennLINC/qsirecon/pull/223

Other Changes

  • Add smoothing and otsu_threshold autotrack arguments by @smeisler in https://github.com/PennLINC/qsirecon/pull/219

  • Allow desc entity in recon scalar derivatives by @tsalo in https://github.com/PennLINC/qsirecon/pull/220

New Contributors

  • @araikes made their first contribution in https://github.com/PennLINC/qsirecon/pull/218

Full Changelog: https://github.com/PennLINC/qsirecon/compare/1.0.1…1.1.0

1.0.1

πŸŽ‰ Exciting New Features

  • Add DSIQ5 extrapolation option by @tsalo in https://github.com/PennLINC/qsirecon/pull/214

πŸ› Bug Fixes

  • Clip negative values in extrapolation interfaces by @tsalo in https://github.com/PennLINC/qsirecon/pull/213

Other Changes

  • Fixes small docs typo: β€œscelar” => β€œscalar” by @arokem in https://github.com/PennLINC/qsirecon/pull/203

  • Fix FA description in DSIStudio outputs by @smeisler in https://github.com/PennLINC/qsirecon/pull/198

New Contributors

  • @arokem made their first contribution in https://github.com/PennLINC/qsirecon/pull/203

Full Changelog: https://github.com/PennLINC/qsirecon/compare/1.0.0…1.0.1

1.0.0

πŸ›  Breaking Changes

  • Rename QSIPrep to QSIRecon by @tsalo in https://github.com/PennLINC/qsirecon/pull/1

  • Start removing QSIPrep-specific code and documentation by @tsalo in https://github.com/PennLINC/qsirecon/pull/4

  • Remove QSIPrep-specific parameters and Config elements by @tsalo in https://github.com/PennLINC/qsirecon/pull/6

  • Drop Docker wrapper by @tsalo in https://github.com/PennLINC/qsirecon/pull/52

  • Restructure outputs into BIDS datasets by @tsalo in https://github.com/PennLINC/qsirecon/pull/66

  • Combine mfp and mdp entities into single param entity by @tsalo in https://github.com/PennLINC/qsirecon/pull/72

  • Replace --recon-input-pipeline with --input-type by @tsalo in https://github.com/PennLINC/qsirecon/pull/68

  • Remove unused --longitudinal argument by @tsalo in https://github.com/PennLINC/qsirecon/pull/88

  • Make all params and models lower-case by @tsalo in https://github.com/PennLINC/qsirecon/pull/90

  • Reorganize atlas management based on XCP-D and BIDS-Atlas by @tsalo in https://github.com/PennLINC/qsirecon/pull/123

  • Rename --freesurfer-input to --fs-subjects-dir by @tsalo in https://github.com/PennLINC/qsirecon/pull/152

  • [ENH] Read session-specific anat data by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/151

  • Remove underscore versions of all parameters by @tsalo in https://github.com/PennLINC/qsirecon/pull/159

  • Make connectivity field names compatible with MATLAB by @tsalo in https://github.com/PennLINC/qsirecon/pull/166

πŸŽ‰ Exciting New Features

  • Add ng, perng, parng, and mapcoeffs to Dipy MAPMRI outputs by @tsalo in https://github.com/PennLINC/qsirecon/pull/55

  • Add DatasetLinks to dataset_description.json by @tsalo in https://github.com/PennLINC/qsirecon/pull/77

  • Pass DWI file metadata to reconstruction workflows by @tsalo in https://github.com/PennLINC/qsirecon/pull/154

  • Add HBCD Release1 recon workflow by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/169

πŸ› Bug Fixes

  • Write out QSIRecon pipeline-wise reports by @tsalo in https://github.com/PennLINC/qsirecon/pull/7

  • Write out reports to individual reconstruction derivative folders by @tsalo in https://github.com/PennLINC/qsirecon/pull/53

  • Add summary reportlets to HTML report by @tsalo in https://github.com/PennLINC/qsirecon/pull/61

  • Fix QSIRecon Entrypoint by @smeisler in https://github.com/PennLINC/qsirecon/pull/76

  • Use file lock to avoid concurrent edits to dataset_description.json by @cookpa in https://github.com/PennLINC/qsirecon/pull/91

  • Compress the tck files by @tsalo in https://github.com/PennLINC/qsirecon/pull/93

  • Add missing filename patterns by @tsalo in https://github.com/PennLINC/qsirecon/pull/131

  • Fix infant anatomical ingression by @tsalo in https://github.com/PennLINC/qsirecon/pull/126

  • Fix extension in ds_fs_5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/165

  • Fix extension in ds_qsiprep_5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/172

  • Fix space in ds_qsiprep_5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/175

  • Make PlotPeaks robust enough that we don’t need –writable-tempfs in singularity/apptainer by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/174

Other Changes

  • Remove internal version of LiterateWorkflow by @tsalo in https://github.com/PennLINC/qsirecon/pull/8

  • Drop and modify infrastructure files by @tsalo in https://github.com/PennLINC/qsirecon/pull/40

  • Remove QSIPrep-specific tests by @tsalo in https://github.com/PennLINC/qsirecon/pull/5

  • Drop unused modules, classes, and functions by @tsalo in https://github.com/PennLINC/qsirecon/pull/11

  • [CI] Speed up pyafq test by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/57

  • [DOCS] Reorganize documentation by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/56

  • Collect templates from TemplateFlow instead of package data by @tsalo in https://github.com/PennLINC/qsirecon/pull/49

  • Remove unused data files by @tsalo in https://github.com/PennLINC/qsirecon/pull/63

  • Replace hyperlinks with BibTeX references by @tsalo in https://github.com/PennLINC/qsirecon/pull/67

  • [DOCS] Add scalar tables by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/80

  • Move scalar file configs to YAMLs and use a recon scalar workflow by @tsalo in https://github.com/PennLINC/qsirecon/pull/79

  • [WIP] Make a system for keeping docs and file names in sync by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/86

  • Convert pipeline configs from JSON to YAML by @tsalo in https://github.com/PennLINC/qsirecon/pull/84

  • [DOCS] clean up by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/101

  • Draft pre-init ingression by @tsalo in https://github.com/PennLINC/qsirecon/pull/102

  • [ENH] Update AMICO by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/115

  • [FIX] mif2fib by @ameliecr in https://github.com/PennLINC/qsirecon/pull/116

  • Fix how bundles to be tracked are selected for DSIstudio autotrack by @ameliecr in https://github.com/PennLINC/qsirecon/pull/121

  • [FIX] workflow connection in dsi_studio_gqi by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/142

  • [CI] add hsvs test by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/136

  • [FIX] dsi_studio_gqi workflow connect by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/146

  • [DOC] Minor addition for skipping connectivity matrices step by @chiuhoward in https://github.com/PennLINC/qsirecon/pull/150

  • Add page documenting output structure by @tsalo in https://github.com/PennLINC/qsirecon/pull/156

  • Add information about QSIPrep/QSIRecon releases by @tsalo in https://github.com/PennLINC/qsirecon/pull/158

  • [CI] Add tests for reading pre-1.0 outputs from qsiprep by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/155

  • [ENH] Support outputs from qsiprep 1.0.0rc0 by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/160

  • [FIX] get rid of logging error #145 by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/161

  • Add UKB ingression by @smeisler in https://github.com/PennLINC/qsirecon/pull/147

  • [FIX] set TMPDIR before running plot_peaks by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/163

  • [ENH] match to qsiprep nipype/nireports versions by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/167

  • Add in Val’s text for connectivity matrices by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/173

  • Disable test_main in the CI integration tests by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/177

New Contributors

  • @tsalo made their first contribution in https://github.com/PennLINC/qsirecon/pull/1

  • @mattcieslak made their first contribution in https://github.com/PennLINC/qsirecon/pull/57

  • @cookpa made their first contribution in https://github.com/PennLINC/qsirecon/pull/91

  • @dependabot made their first contribution in https://github.com/PennLINC/qsirecon/pull/100

  • @ameliecr made their first contribution in https://github.com/PennLINC/qsirecon/pull/116

  • @chiuhoward made their first contribution in https://github.com/PennLINC/qsirecon/pull/150

Full Changelog: https://github.com/PennLINC/qsirecon/commits/1.0.0