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#diffusion models Open access

QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI

Matthew Cieslak Taylor Salo Philip A. Cook Paul Camacho Sydney C. Covitz Will Foran Xiaosong He Joseph Humphries Aaron Kaluszka J. Legarreta Fredrik Magnussen Steven L. Meisler Lucille A. Moore Michael Krause Patrick S. Sadil Valerie J. Sydnor Theodore Daniel Satterthwaite
Sep 2026 · Zenodo (CERN European Organization for Nuclear Research)

Abstract

<!-- Release notes generated using configuration in .github/release.yml at main --> What's Changed 🛠 Breaking Changes Redo the scan grouping so it uses modern BIDS and is easier to understand by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1092 Rename --session-id to --session-label by @tsalo in https://github.com/PennLINC/qsiprep/pull/1136 Remove --longitudinal parameter by @tsalo in https://github.com/PennLINC/qsiprep/pull/1126 Remove --prefer-dedicated-fmaps parameter by @tsalo in https://github.com/PennLINC/qsiprep/pull/1125 Remove --b0-motion-correct-to parameter by @tsalo in https://github.com/PennLINC/qsiprep/pull/1124 Remove --dwi-only, --dwi-no-biascorr, and --fs-license-file by @tsalo in https://github.com/PennLINC/qsiprep/pull/1145 Rename --dwi-denoise-window to --dwidenoise-window by @tsalo in https://github.com/PennLINC/qsiprep/pull/1149 Remove --denoise-after-combining by @tsalo in https://github.com/PennLINC/qsiprep/pull/1146 Rename CLI parameters by @tsalo in https://github.com/PennLINC/qsiprep/pull/1144 Remove --anat-only flag by @tsalo in https://github.com/PennLINC/qsiprep/pull/1151 Remove first-alphabetically option from --subject-anatomical-reference by @tsalo in https://github.com/PennLINC/qsiprep/pull/1157 Replace dwidenoise2 parameter parsing with config file by @tsalo in https://github.com/PennLINC/qsiprep/pull/1156 🎉 Exciting New Features Add TORTOISE DIFFPREP as a head-motion-correction backend by @tsalo in https://github.com/PennLINC/qsiprep/pull/1066 Add dwidenoise2 denoising option by @tsalo in https://github.com/PennLINC/qsiprep/pull/1071 Add --report-output-level CLI argument by @tsalo in https://github.com/PennLINC/qsiprep/pull/1087 Add new gradient plot to htmls by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1104 Make MRtrix development version available with --mrtrix-version by @tsalo in https://github.com/PennLINC/qsiprep/pull/1110 Support gradient unwarping with TORTOISE by @tsalo in https://github.com/PennLINC/qsiprep/pull/1106 Allow users to specify 3D or 1D (through-plane) gradient distortion correction by @tsalo in https://github.com/PennLINC/qsiprep/pull/1135 Add white matter boundary to coregistration figure by @tsalo in https://github.com/PennLINC/qsiprep/pull/1115 Add SDC displacement maps and figures to derivatives by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1154 Apply Jacobian weighting to all spatial distortion corrections by @tsalo in https://github.com/PennLINC/qsiprep/pull/1147 Use GRE fieldmaps inside eddy and to initialize DRBUDDI and T2Wreg by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1159 Add --force no-csf-synthstrip for the template registration mask by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1162 🐛 Bug Fixes Replace zero-magnitude b-vectors with [1 0 0] by @tsalo in https://github.com/PennLINC/qsiprep/pull/1059 Monkeypatch create_cfm to use LPS lesion mask by @tsalo in https://github.com/PennLINC/qsiprep/pull/1058 Add flexible check for available CUDA version by @tsalo in https://github.com/PennLINC/qsiprep/pull/1057 Retain magnitude data for complex-valued dwidenoise reportlet by @tsalo in https://github.com/PennLINC/qsiprep/pull/1055 Set minimum dwi_denoise_window to 3 by @tsalo in https://github.com/PennLINC/qsiprep/pull/1064 Address inheritance failures by @tsalo in https://github.com/PennLINC/qsiprep/pull/1080 Use template shape and resolution in anatomical reportlet by @tsalo in https://github.com/PennLINC/qsiprep/pull/1098 Make sure motion parameters are reported in the same convention for tortoise and eddy by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1084 Use same cropped FOV for before and after images in reportlets by @tsalo in https://github.com/PennLINC/qsiprep/pull/1100 Update TORTOISE for Gibbs bugfixes by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1101 Enforce fixed FOV in figures with context manager by @tsalo in https://github.com/PennLINC/qsiprep/pull/1119 Remove --fmap-bspline parameter by @tsalo in https://github.com/PennLINC/qsiprep/pull/1131 Remove unused --fmap-no-demean parameter by @tsalo in https://github.com/PennLINC/qsiprep/pull/1130 Stop DWI summary reportlet duplication by @tsalo in https://github.com/PennLINC/qsiprep/pull/1113 Raise an exception if no files are found for sessions in --session-id by @tsalo in https://github.com/PennLINC/qsiprep/pull/1121 Fix eddy cuda finding by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1158 Other Changes Streamline CircleCI by @tsalo in https://github.com/PennLINC/qsiprep/pull/1049 Fix CircleCI by @tsalo in https://github.com/PennLINC/qsiprep/pull/1056 Consistently use acres like other BIDS Apps by @tsalo in https://github.com/PennLINC/qsiprep/pull/1060 Document --ignore fieldmaps by @tsalo in https://github.com/PennLINC/qsiprep/pull/1065 Rename figures to follow fMRIPrep's convention by @tsalo in https://github.com/PennLINC/qsiprep/pull/1062 Configure shared libraries for DSIStudio commands at runtime by @tsalo in https://github.com/PennLINC/qsiprep/pull/1073 Sync CI setup across LINC BIDS Apps by @tsalo in https://github.com/PennLINC/qsiprep/pull/1075 Anat biascorr masks by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1078 Raise deprecation warnings for deprecated parameters by @tsalo in https://github.com/PennLINC/qsiprep/pull/1083 Replace hyperlink-based references by @tsalo in https://github.com/PennLINC/qsiprep/pull/1088 Update Python to 3.11 and DIPY to 1.12 by @tsalo in https://github.com/PennLINC/qsiprep/pull/1077 Rename "diffprep" HMC model options to "tortoise" by @tsalo in https://github.com/PennLINC/qsiprep/pull/1085 Clean up intramodal template workflows and add boilerplate text by @tsalo in https://github.com/PennLINC/qsiprep/pull/1095 Fix diffprep boilerplate text by @tsalo in https://github.com/PennLINC/qsiprep/pull/1102 Control threading in Gibbs by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1103 Introduce the "workflow compiler" by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1105 Use TORTOISE's best b=0 picker by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1107 Add synb0 and reorganize sdc cli options by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1111 Read the part-phase companions from qsiplan by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1116 Use ants Affine Initializer (antsAI) for coregistration by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1118 Replace FUGUE and PRELUDE with niimath by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1139 Clean up arguments for HMC by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1140 Handle git annex files correctly when imported from qsiplan by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1112 Reorganize CLI arguments by @tsalo in https://github.com/PennLINC/qsiprep/pull/1142 Set NIFTI_INTENT_VECTOR on the synthetic ITK displacement field fixture by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1153 Fix unit test by @tsalo in https://github.com/PennLINC/qsiprep/pull/1161 Use numpydoc convention for all docstrings by @tsalo in https://github.com/PennLINC/qsiprep/pull/1160 FIX: Keep the T2w at its own resolution for DRBUDDI; SynB0 TOPUP on odd dimensions by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1164 Overhaul docs for 26.1.0 by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/1163 Full Changelog: https://github.com/PennLINC/qsiprep/compare/26.0.0...26.1.0rc1

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