PreQual

Integrated preprocessing and quality assurance of diffusion weighted MRI

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Vanderbilt License

PreQual can invoke Synb0-DisCo to correct susceptibility-induced distortions without reverse phase-encoded images or field maps.

PreQual is an automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI (dMRI) images. It combines MP-PCA denoising, distortion and motion correction, and bias-field correction with an extensive battery of quality assurance metrics.

Usage

With the diffusion MRI files (.nii.gz, .bval, and .bvec) and a dtiQA_config.csv configuration file in ./input, and an empty ./output directory. A pre-built container is available on Zenodo (DOI: 10.5281/zenodo.18624309):

apptainer run \
    -e \
    --contain \
    --home ./input \
    -B ./input:/INPUTS \
    -B ./output:/OUTPUTS \
    -B /tmp:/tmp \
    ./prequal.simg \
    i

Replace i with the phase-encoding axis for your data (i or j). To enable Synb0-DisCo distortion correction or GPU-accelerated eddy, additionally bind the FreeSurfer license (-B /path/to/license.txt:/APPS/freesurfer/license.txt) and CUDA (--nv -B /path/to/cuda:/usr/local/cuda), as described in the repository README.

The final preprocessed volume will be in ./output/PREPROCESSED/dwmri.nii.gz, and the quality assurance report will be in ./output/PDF/dtiQA.pdf.

Config file

dtiQA_config.csv (which must be named exactly) contains one line per input image, giving the shared file prefix, the phase-encoding direction, and the readout time:

Column	Description	Example
image	Shared file prefix of the corresponding .nii.gz, .bval, and .bvec files (no path)	dti1
pe_dir	Phase-encoding direction along the axis given above: + or -	+
readout_time	Effective readout time (seconds) used to scale the estimated b0 field in FSL’s eddy; 0 means infinite bandwidth (no susceptibility distortion)	0.05

For two images in ./input:

dti1,+,0.05
dti2,+,0.05

Note that the phase-encoding axis, direction, and readout time are not stored in NIFTI headers, so they must be known in advance (for example, from the scan protocol or the JSON sidecars created when converting DICOMs with dcm2niix).

Leon Y. Cai, Qi Yang, Colin B. Hansen, Vishwesh Nath, Karthik Ramadass, Graham W. Johnson, Benjamin N. Conrad, Brian D. Boyd, John P. Begnoche, Lori L. Beason-Held, Andrea T. Shafer, Susan M. Resnick, Warren D. Taylor, Gavin R. Price, Victoria L. Morgan, Baxter P. Rogers, Kurt G. Schilling, and Bennett A. Landman. “PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images” Magnetic Resonance in Medicine, 2021.