1.1.1

This release fixes a major bug in QSIRecon's handling of multi-session and multi-run datasets. When processing multiple sessions or runs in a single QSIRecon call, the reconstruction workflow was being modified in place, such that the first session/run was processed correctly, but subsequent sessions/runs were processed with global default values. This bug primarily affected custom reconstruction workflows. The built-in workflows should be largely unaffected.

What's Changed

🎉 Exciting New Features

• Parcellate scalars and write out brain mask by @tsalo in #251
• Use deltas in DIPY interfaces by @tsalo in #259

🐛 Bug Fixes

• Upgrade DIPY, pyAFQ by @36000 in #235
• Fix handling of atlas labels with spaces and test custom atlas handling by @tsalo in #248
• Remove background label from atlases before calculating connectivity by @tsalo in #249
• Fix collection of longitudinal anatomical outputs by @tsalo in #253
• Write out ACPC-space scalars from TORTOISE node if estimate_mapmri is False by @tsalo in #254
• Prevent workflow spec dictionary from being modified in place during build process by @tsalo in #263

Other Changes

• Update boilerplate.bib for mrtrix reference by @chiuhoward in #239
• Update descriptions of scalar map parameters by @tsalo in #225
• Generate figure showing scalar maps by @tsalo in #246
• Remove outdated admonition by @tsalo in #257
• Add missing workflows to "which workflows are appropriate" table by @tsalo in #258
• Fix table borders by @tsalo in #260
• Add unused plot_reports input to _KurtosisReconstructionInputSpec by @tsalo in #262

New Contributors

• @36000 made their first contribution in #235

Full Changelog: 1.1.0...1.1.1

1.1.0

What's Changed

🎉 Exciting New Features

• Tissue fraction modulated ICVF and OD maps by @araikes in #218
• Calculate kurtosis microstructure scalars with new DKI_reconstruction parameter by @tsalo in #223

Other Changes

• Add smoothing and otsu_threshold autotrack arguments by @smeisler in #219
• Allow desc entity in recon scalar derivatives by @tsalo in #220

New Contributors

• @araikes made their first contribution in #218

Full Changelog: 1.0.1...1.1.0

1.0.1

What's Changed

🎉 Exciting New Features

• Add DSIQ5 extrapolation option by @tsalo in #214

🐛 Bug Fixes

• Clip negative values in extrapolation interfaces by @tsalo in #213

Other Changes

• Fixes small docs typo: "scelar" => "scalar" by @arokem in #203
• Fix FA description in DSIStudio outputs by @smeisler in #198

New Contributors

• @arokem made their first contribution in #203

Full Changelog: 1.0.0...1.0.1

1.0.0

What's Changed

🛠 Breaking Changes

• 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

• Pass DWI file metadata to reconstruction workflows by @tsalo in #154
• Add HBCD Release1 recon workflow by @mattcieslak in #169
• Support output spaces to arbitrary templates and cohorts by @mattcieslak in #184

🐛 Bug Fixes

• 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
• Use abspaths for the ODF plotter by @mattcieslak in #182

Other Changes

• [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
• Link to NiPreps contributing guidelines by @LuciMoore in #193
• Add a node for selecting specific shells from preprocessed dwis by @mattcieslak in #194
• Add official recon spec for ss3t FOD autotrack by @mattcieslak in #196
• Add Chen version as an option for autotrack by @mattcieslak in #201
• Switch hbcd pipeline back to Chen by @mattcieslak in #202

New Contributors

• @chiuhoward made their first contribution in #150
• @LuciMoore made their first contribution in #193

Full Changelog: 0.23.2...1.0.0

1.0.0rc2

What's Changed

🎉 Exciting New Features

• Support output spaces to arbitrary templates and cohorts by @mattcieslak in #184

🐛 Bug Fixes

• Use abspaths for the ODF plotter by @mattcieslak in #182

Full Changelog: 1.0.0rc1...1.0.0rc2

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 #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

New Contributors

• @tsalo made their first contribution in #1
• @mattcieslak made their first contribution in #57
• @cookpa made their first contribution in #91
• @dependabot made their first contribution in #100
• @ameliecr made their first contribution in #116
• @chiuhoward made their first contribution in #150

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