Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of qsirecon

qsirecon - 1.1.0

What's Changed

🎉 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

- Python
Published by tsalo 11 months ago

qsirecon - 1.0.1

What's Changed

🎉 Exciting New Features

  • Add DSIQ5 extrapolation option by @tsalo in https://github.com/PennLINC/qsirecon/pull/214 ### 🐛 Bug Fixes
  • Clip negative values in extrapolation interfaces by @tsalo in https://github.com/PennLINC/qsirecon/pull/213 ### Other Changes
  • Fixes small docs typo: "scelar" => "scalar" 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

- Python
Published by tsalo 12 months ago

qsirecon - 1.0.0

What's Changed

🛠 Breaking Changes

  • 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 ### 🎉 Exciting New Features
  • 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
  • Support output spaces to arbitrary templates and cohorts by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/184 ### 🐛 Bug Fixes
  • 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 dsfs5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/165
  • Fix extension in dsqsiprep5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/172
  • Fix space in dsqsiprep5tt_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
  • Use abspaths for the ODF plotter by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/182 ### Other Changes
  • [FIX] workflow connection in dsistudiogqi 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] dsistudiogqi 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
  • Link to NiPreps contributing guidelines by @LuciMoore in https://github.com/PennLINC/qsirecon/pull/193
  • Add a node for selecting specific shells from preprocessed dwis by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/194
  • Add official recon spec for ss3t FOD autotrack by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/196
  • Add Chen version as an option for autotrack by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/201
  • Switch hbcd pipeline back to Chen by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/202

New Contributors

  • @chiuhoward made their first contribution in https://github.com/PennLINC/qsirecon/pull/150
  • @LuciMoore made their first contribution in https://github.com/PennLINC/qsirecon/pull/193

Full Changelog: https://github.com/PennLINC/qsirecon/compare/0.23.2...1.0.0

- Python
Published by tsalo 12 months ago

qsirecon - 1.0.0rc2

What's Changed

🎉 Exciting New Features

  • Support output spaces to arbitrary templates and cohorts by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/184

🐛 Bug Fixes

  • Use abspaths for the ODF plotter by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/182

Full Changelog: https://github.com/PennLINC/qsirecon/compare/1.0.0rc1...1.0.0rc2

- Python
Published by tsalo over 1 year ago

qsirecon - 1.0.0rc1

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 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

🎉 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

🐛 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 dsfs5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/165
  • Fix extension in dsqsiprep5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/172
  • Fix space in dsqsiprep5tt_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 dsistudiogqi 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] dsistudiogqi 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/1.0.0rc1

- Python
Published by tsalo over 1 year ago