Upgrading from 26.0

26.1 reorganized the command line. Options are now grouped by decision in --help, several were renamed, and options whose settings moved into a configuration file were removed. Run qsiprep --help or see Command-line reference for the current list.

Removed or renamed options

In 26.0

In 26.1

PR

--session-id

--session-label

#1136

--dwi-only

--anat-modality none

#1145

--dwi-no-biascorr, --b1-biascorrect-stage

--dwi-biascorrect none (or n4, auto)

#1145, #1144

--fs-license-file

Removed. No FreeSurfer license is needed.

#1145

--dwi-denoise-window

--dwidenoise-window

#1149

--denoise-after-combining

Removed. Series are always denoised before concatenation.

#1146

--anat-only

Removed.

#1151

--hmc-model eddy

--hmc-method eddy

#1105

--hmc-model none, 3dSHORE or tensor

--hmc-method shoreline, with the model in --shoreline-config

#1105, #1140

--hmc-transform, --shoreline-iters

--shoreline-config (a JSON file; see Configuring SHORELine)

#1140

--pepolar-method

--sdc-method

#1140

--force-syn, --use-syn-sdc

--sdc-anat-reference invt1w, with --force sdc-anat-reference to override fieldmaps

#1111

--b0-to-t1w-transform

--dwi2anat-dof 6 (rigid) or 12 (affine)

#1144

--intramodal-template-iters, --intramodal-template-transform

--dwiref-definition subject with --dwiref-construction-iters and --dwiref-construction-transform

#1144

--longitudinal

--subject-anatomical-reference unbiased

#1126

--subject-anatomical-reference first-alphabetically

--subject-anatomical-reference first-lex

#1157

--b0-motion-corr-to, --fmap-no-demean, --fmap-bspline

Removed.

#1124, #1130, #1131

New options

  • --hmc-method tortoise and --diffprep-config: TORTOISE DIFFPREP head motion and eddy-current correction (TORTOISE DIFFPREP).

  • --sdc-method: topup, drbuddi or topup+drbuddi for reverse phase-encoded data (Susceptibility distortion correction).

  • --sdc-anat-reference: synb0, t2w, invt1w or auto fieldmap-less correction as a fallback, and --force sdc-anat-reference.

  • --gradient-file, --force gradwarp1D/gradwarp3D, --ignore gradwarp: gradient nonlinearity correction (Gradient nonlinearity correction).

  • --ignore jacobian, --force jacobian: intensity modulation after distortion correction (Intensity modulation).

  • --gpu and --tortoise-gpu-cpu-ratio: per-task GPU selection, replacing use_cuda in the configuration files.

  • --denoise-method dwidenoise2, --denoise-method svht, --unringing-method svht and --denoise-config.

  • --mrtrix-version: use the MRtrix3 development branch.

  • --anat-biascorrect, --report-output-level, --ignore t2w, --ignore phase, --ignore shims, --ignore fov.

Behavior changes

  • Grouping is done by qsiplan. The rules for which scans estimate a fieldmap, which fieldmap corrects which scan and which scans are concatenated are now shared with the standalone qsiplan tool, and every decision is reported with its provenance. B0FieldIdentifier and B0FieldSource are supported, and BIDS URIs work in IntendedFor. Inconsistent metadata that used to be silently worked around now stops the run with a named error (Grouping and metadata errors).

  • GRE fieldmaps go into eddy. With --hmc-method eddy, a GRE fieldmap is passed to eddy and applied inside its model rather than to its outputs. --force gre-sdc-after-eddy restores the old behavior for comparison and is deprecated.

  • A GRE fieldmap initializes DRBUDDI and T2Wreg when a series is also corrected by reverse phase encoding (Initializing DRBUDDI and T2Wreg from a GRE fieldmap).

  • Intensity modulation after distortion correction is now applied by QSIPrep for the corrections it resamples itself, and written as a derivative.

  • Distortion correction displacement maps are written for inspection.

  • GRE fieldmaps no longer use FSL. Phase unwrapping and fieldmap application use niimath’s ROMEO implementation instead of PRELUDE and FUGUE.

  • SHORELine is deprecated and prints a removal notice.

  • Output naming follows fMRIPrep 26.0 for the coregistration reference: space-distortiongroup or space-subject on the reference image and desc-coreg on the transforms (Transforms).