26.1.0rc1

[tsalo]

What's Changed

🛠 Breaking Changes

• Redo the scan grouping so it uses modern BIDS and is easier to understand by @mattcieslak in Redo the scan grouping so it uses modern BIDS and is easier to understand #1092
• Rename --session-id to --session-label by @tsalo in Rename --session-id to --session-label #1136
• Remove --longitudinal parameter by @tsalo in Remove --longitudinal parameter #1126
• Remove --prefer-dedicated-fmaps parameter by @tsalo in Remove --prefer-dedicated-fmaps parameter #1125
• Remove --b0-motion-correct-to parameter by @tsalo in Remove --b0-motion-correct-to parameter #1124
• Remove --dwi-only, --dwi-no-biascorr, and --fs-license-file by @tsalo in Remove --dwi-only, --dwi-no-biascorr, and --fs-license-file #1145
• Rename --dwi-denoise-window to --dwidenoise-window by @tsalo in Rename --dwi-denoise-window to --dwidenoise-window #1149
• Remove --denoise-after-combining by @tsalo in Remove --denoise-after-combining #1146
• Rename CLI parameters by @tsalo in Rename CLI parameters #1144
• Remove --anat-only flag by @tsalo in Remove --anat-only flag #1151
• Remove first-alphabetically option from --subject-anatomical-reference by @tsalo in Remove first-alphabetically option from --subject-anatomical-reference #1157
• Replace dwidenoise2 parameter parsing with config file by @tsalo in Replace dwidenoise2 parameter parsing with config file #1156

🎉 Exciting New Features

• Add TORTOISE DIFFPREP as a head-motion-correction backend by @tsalo in Add TORTOISE DIFFPREP as a head-motion-correction backend #1066
• Add dwidenoise2 denoising option by @tsalo in Add dwidenoise2 denoising option #1071
• Add --report-output-level CLI argument by @tsalo in Add --report-output-level CLI argument #1087
• Add new gradient plot to htmls by @mattcieslak in Add new gradient plot to htmls #1104
• Make MRtrix development version available with --mrtrix-version by @tsalo in Make MRtrix development version available with --mrtrix-version #1110
• Support gradient unwarping with TORTOISE by @tsalo in Support gradient unwarping with TORTOISE #1106
• Allow users to specify 3D or 1D (through-plane) gradient distortion correction by @tsalo in Allow users to specify 3D or 1D (through-plane) gradient distortion correction #1135
• Add white matter boundary to coregistration figure by @tsalo in Add white matter boundary to coregistration figure #1115
• Add SDC displacement maps and figures to derivatives by @mattcieslak in Add SDC displacement maps and figures to derivatives #1154
• Apply Jacobian weighting to all spatial distortion corrections by @tsalo in Apply Jacobian weighting to all spatial distortion corrections #1147
• Use GRE fieldmaps inside eddy and to initialize DRBUDDI and T2Wreg by @mattcieslak in Use GRE fieldmaps inside eddy and to initialize DRBUDDI and T2Wreg #1159
• Add --force no-csf-synthstrip for the template registration mask by @mattcieslak in Add --force no-csf-synthstrip for the template registration mask #1162

🐛 Bug Fixes

• Replace zero-magnitude b-vectors with [1 0 0] by @tsalo in Replace zero-magnitude b-vectors with [1 0 0] #1059
• Monkeypatch create_cfm to use LPS lesion mask by @tsalo in Monkeypatch create_cfm to use LPS lesion mask #1058
• Add flexible check for available CUDA version by @tsalo in Add flexible check for available CUDA version #1057
• Retain magnitude data for complex-valued dwidenoise reportlet by @tsalo in Retain magnitude data for complex-valued dwidenoise reportlet #1055
• Set minimum dwi_denoise_window to 3 by @tsalo in Set minimum dwi_denoise_window to 3 #1064
• Address inheritance failures by @tsalo in Address inheritance failures #1080
• Use template shape and resolution in anatomical reportlet by @tsalo in Use template shape and resolution in anatomical reportlet #1098
• Make sure motion parameters are reported in the same convention for tortoise and eddy by @mattcieslak in Make sure motion parameters are reported in the same convention for tortoise and eddy #1084
• Use same cropped FOV for before and after images in reportlets by @tsalo in Use same cropped FOV for before and after images in reportlets #1100
• Update TORTOISE for Gibbs bugfixes by @mattcieslak in Update TORTOISE for Gibbs bugfixes #1101
• Enforce fixed FOV in figures with context manager by @tsalo in Enforce fixed FOV in figures with context manager #1119
• Remove --fmap-bspline parameter by @tsalo in Remove --fmap-bspline parameter #1131
• Remove unused --fmap-no-demean parameter by @tsalo in Remove unused --fmap-no-demean parameter #1130
• Stop DWI summary reportlet duplication by @tsalo in Stop DWI summary reportlet duplication #1113
• Raise an exception if no files are found for sessions in --session-id by @tsalo in Raise an exception if no files are found for sessions in --session-id #1121
• Fix eddy cuda finding by @mattcieslak in Fix eddy cuda finding #1158

Other Changes

• Streamline CircleCI by @tsalo in Streamline CircleCI #1049
• Fix CircleCI by @tsalo in Fix CircleCI #1056
• Consistently use acres like other BIDS Apps by @tsalo in Consistently use acres like other BIDS Apps #1060
• Document --ignore fieldmaps by @tsalo in Document --ignore fieldmaps #1065
• Rename figures to follow fMRIPrep's convention by @tsalo in Rename figures to follow fMRIPrep's convention #1062
• Configure shared libraries for DSIStudio commands at runtime by @tsalo in Configure shared libraries for DSIStudio commands at runtime #1073
• Sync CI setup across LINC BIDS Apps by @tsalo in Sync CI setup across LINC BIDS Apps #1075
• Anat biascorr masks by @mattcieslak in Anat biascorr masks #1078
• Raise deprecation warnings for deprecated parameters by @tsalo in Raise deprecation warnings for deprecated parameters #1083
• Replace hyperlink-based references by @tsalo in Replace hyperlink-based references #1088
• Update Python to 3.11 and DIPY to 1.12 by @tsalo in Update Python to 3.11 and DIPY to 1.12 #1077
• Rename "diffprep" HMC model options to "tortoise" by @tsalo in Rename "diffprep" HMC model options to "tortoise" #1085
• Clean up intramodal template workflows and add boilerplate text by @tsalo in Clean up intramodal template workflows and add boilerplate text #1095
• Fix diffprep boilerplate text by @tsalo in Fix diffprep boilerplate text #1102
• Control threading in Gibbs by @mattcieslak in Control threading in Gibbs #1103
• Introduce the "workflow compiler" by @mattcieslak in Introduce the "workflow compiler" #1105
• Use TORTOISE's best b=0 picker by @mattcieslak in Use TORTOISE's best b=0 picker #1107
• Add synb0 and reorganize sdc cli options by @mattcieslak in Add synb0 and reorganize sdc cli options #1111
• Read the part-phase companions from qsiplan by @mattcieslak in Read the part-phase companions from qsiplan #1116
• Use ants Affine Initializer (antsAI) for coregistration by @mattcieslak in Use ants Affine Initializer (antsAI) for coregistration #1118
• Replace FUGUE and PRELUDE with niimath by @mattcieslak in Replace FUGUE and PRELUDE with niimath #1139
• Clean up arguments for HMC by @mattcieslak in Clean up arguments for HMC #1140
• Handle git annex files correctly when imported from qsiplan by @mattcieslak in Handle git annex files correctly when imported from qsiplan #1112
• Reorganize CLI arguments by @tsalo in Reorganize CLI arguments #1142
• Set NIFTI_INTENT_VECTOR on the synthetic ITK displacement field fixture by @mattcieslak in Set NIFTI_INTENT_VECTOR on the synthetic ITK displacement field fixture #1153
• Fix unit test by @tsalo in Fix unit test #1161
• Use numpydoc convention for all docstrings by @tsalo in Use numpydoc convention for all docstrings #1160
• FIX: Keep the T2w at its own resolution for DRBUDDI; SynB0 TOPUP on odd dimensions by @mattcieslak in FIX: Keep the T2w at its own resolution for DRBUDDI; SynB0 TOPUP on odd dimensions #1164
• Overhaul docs for 26.1.0 by @mattcieslak in Overhaul docs for 26.1.0 #1163

Full Changelog: 26.0.0...26.1.0rc1

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This discussion was created from the release 26.1.0rc1.