What’s New

1.2.0

🛠 Breaking Changes

• Disable dkimicro/wmti in recon specs by @tsalo in https://github.com/PennLINC/qsirecon/pull/268

🎉 Exciting New Features

• Calculate MD from TORTOISE tensor fits by @tsalo in https://github.com/PennLINC/qsirecon/pull/315

• Raise error if atlases are not collected by @tsalo in https://github.com/PennLINC/qsirecon/pull/256

• Add integer downsample option for MRtrix3 tckgen by @kjamison in https://github.com/PennLINC/qsirecon/pull/324

• Add MSDKI option to DIPY_Reconstruction action by @tsalo in https://github.com/PennLINC/qsirecon/pull/269

• Add missing GQI scalars by @tsalo in https://github.com/PennLINC/qsirecon/pull/326

• Add pipeline description to boilerplate by @tsalo in https://github.com/PennLINC/qsirecon/pull/332

• Add QSIRecon suffix to boilerplate sections and add boilerplates for smaller workflows by @tsalo in https://github.com/PennLINC/qsirecon/pull/331

• Ingress response functions by @tsalo in https://github.com/PennLINC/qsirecon/pull/335

🐛 Bug Fixes

• Account for Query.NONE session IDs in Freesurfer folder detection by @tsalo in https://github.com/PennLINC/qsirecon/pull/271

• Add plot_reports param to failing interfaces by @tsalo in https://github.com/PennLINC/qsirecon/pull/286

• Fix DSI Studio GQI connectivity by @araikes in https://github.com/PennLINC/qsirecon/pull/277

• Fix bug in assignment of formatted LUTs for connectivity steps by @tsalo in https://github.com/PennLINC/qsirecon/pull/278

• Fix parameter assignments in Dipy MAPMRI workflow and document params by @tsalo in https://github.com/PennLINC/qsirecon/pull/308

• Make missing Freesurfer license error messages more informative by @tsalo in https://github.com/PennLINC/qsirecon/pull/261

Other Changes

• Fix workflow reference in builtin_workflows.rst by @appukuttan-shailesh in https://github.com/PennLINC/qsirecon/pull/285

• Add unit metadata to some scalar maps by @tsalo in https://github.com/PennLINC/qsirecon/pull/247

• Clean up the Bibtex file by @araikes in https://github.com/PennLINC/qsirecon/pull/290

• Add scalar params to JSON files by @tsalo in https://github.com/PennLINC/qsirecon/pull/292

• Add parameter metadata extracted from interfaces to boilerplate for tortoise by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/291

• Add model metadata with description and URL reference for MAPMRI by @chiuhoward in https://github.com/PennLINC/qsirecon/pull/295

• Add new available models pages to documentation by @singlesp in https://github.com/PennLINC/qsirecon/pull/306

• Simplify the parameter metadata extraction for JSONs by @tsalo in https://github.com/PennLINC/qsirecon/pull/307

• Add API documentation by @tsalo in https://github.com/PennLINC/qsirecon/pull/233

• Document hardcoded DKI parameters in YAMLs by @cookpa in https://github.com/PennLINC/qsirecon/pull/302

• Add detailed information about DTI to model page by @tien-tong in https://github.com/PennLINC/qsirecon/pull/310

• Add DKI model page to docs by @singlesp in https://github.com/PennLINC/qsirecon/pull/309

• Add parameter metadata extracted from interfaces to boilerplate for AMICO by @araikes in https://github.com/PennLINC/qsirecon/pull/299

• Add GQI model page to docs by @singlesp in https://github.com/PennLINC/qsirecon/pull/311

• Add MAP-MRI model page to docs by @tien-tong in https://github.com/PennLINC/qsirecon/pull/313

• Add noddi model docs by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/325

• Further model docs cleanup by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/327

• Add BIDS metadata to SH fits from mrtrix by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/297

• Make model page markup consistent by @tsalo in https://github.com/PennLINC/qsirecon/pull/329

• DWI only fix by @smeisler in https://github.com/PennLINC/qsirecon/pull/209

• Fix container image name in documentation by @hfxcarl in https://github.com/PennLINC/qsirecon/pull/197

• Make ABCD recon spec built in by @smeisler in https://github.com/PennLINC/qsirecon/pull/344

• Add AGENTS.md and cursor rules by @singlesp in https://github.com/PennLINC/qsirecon/pull/348

• update to ubuntu22.04 by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/343

New Contributors

• @appukuttan-shailesh made their first contribution in https://github.com/PennLINC/qsirecon/pull/285

• @kjamison made their first contribution in https://github.com/PennLINC/qsirecon/pull/324

• @hfxcarl made their first contribution in https://github.com/PennLINC/qsirecon/pull/197

Full Changelog: https://github.com/PennLINC/qsirecon/compare/1.1.1…1.2.0

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.

🎉 Exciting New Features

• Parcellate scalars and write out brain mask by @tsalo in https://github.com/PennLINC/qsirecon/pull/251

• Use deltas in DIPY interfaces by @tsalo in https://github.com/PennLINC/qsirecon/pull/259

🐛 Bug Fixes

• Upgrade DIPY, pyAFQ by @36000 in https://github.com/PennLINC/qsirecon/pull/235

• Fix handling of atlas labels with spaces and test custom atlas handling by @tsalo in https://github.com/PennLINC/qsirecon/pull/248

• Remove background label from atlases before calculating connectivity by @tsalo in https://github.com/PennLINC/qsirecon/pull/249

• Fix collection of longitudinal anatomical outputs by @tsalo in https://github.com/PennLINC/qsirecon/pull/253

• Write out ACPC-space scalars from TORTOISE node if estimate_mapmri is False by @tsalo in https://github.com/PennLINC/qsirecon/pull/254

• Prevent workflow spec dictionary from being modified in place during build process by @tsalo in https://github.com/PennLINC/qsirecon/pull/263

Other Changes

• Update boilerplate.bib for mrtrix reference by @chiuhoward in https://github.com/PennLINC/qsirecon/pull/239

• Update descriptions of scalar map parameters by @tsalo in https://github.com/PennLINC/qsirecon/pull/225

• Generate figure showing scalar maps by @tsalo in https://github.com/PennLINC/qsirecon/pull/246

• Remove outdated admonition by @tsalo in https://github.com/PennLINC/qsirecon/pull/257

• Add missing workflows to “which workflows are appropriate” table by @tsalo in https://github.com/PennLINC/qsirecon/pull/258

• Fix table borders by @tsalo in https://github.com/PennLINC/qsirecon/pull/260

• Add unused plot_reports input to _KurtosisReconstructionInputSpec by @tsalo in https://github.com/PennLINC/qsirecon/pull/262

New Contributors

• @36000 made their first contribution in https://github.com/PennLINC/qsirecon/pull/235

Full Changelog: https://github.com/PennLINC/qsirecon/compare/1.1.0…1.1.1

1.1.0

🎉 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

🎉 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

1.0.0

🛠 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 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