What’s New

26.0.0 (April 20, 2026)

πŸ›  Breaking Changes

  • Bring packaging in line with NiPreps and adopt BIDS atlas organization by @tsalo in https://github.com/PennLINC/qsirecon/pull/367

πŸ› Bug Fixes

  • Allow schemes to be classified as β€œunknown” by @tsalo in https://github.com/PennLINC/qsirecon/pull/364

  • Replace np.complex with complex by @tsalo in https://github.com/PennLINC/qsirecon/pull/372

  • Change shutil.copy to shutil.copyfile by @tsalo in https://github.com/PennLINC/qsirecon/pull/373

  • Make --recon-spec a required argument by @tsalo in https://github.com/PennLINC/qsirecon/pull/375

Other Changes

  • Migrate from flake8 + black + isort to ruff by @tsalo in https://github.com/PennLINC/qsirecon/pull/351

  • Address easy style issues by @tsalo in https://github.com/PennLINC/qsirecon/pull/352

  • Fix version string issue by @tsalo in https://github.com/PennLINC/qsirecon/pull/355

  • Add tox, pre-commit config, and dependabot by @tsalo in https://github.com/PennLINC/qsirecon/pull/353

  • Address Sphinx build issues by @tsalo in https://github.com/PennLINC/qsirecon/pull/366

  • Remove undefined FSFAST_HOME variable by @tsalo in https://github.com/PennLINC/qsirecon/pull/376

Full Changelog: https://github.com/PennLINC/qsirecon/compare/1.2.0…26.0.0

1.2.0 (February 18, 2026)

πŸ›  Breaking Changes

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

πŸŽ‰ 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

πŸ› 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 (August 19, 2025)

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.

πŸŽ‰ 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

πŸ› 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 β€œwhich 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 (April 14, 2025)

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 (March 12, 2025)

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 (March 11, 2025)

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