List of Flags

PyDesigner is extremely flexible when it comes to dMRI processing. Users can easily enable or disable various preprocessing steps without changing the overall sequence.

The list below covers all these flags.

IO Control

These flags allow control of the pipeline’s I/O handling

-o DIR, --output DIR

PyDesigner output directory

Preprocessing Control

Preprocessing contol flags allow users to tweak certain parts of the preprocessing pipeline, to accomodate all types of datasets.

-s, --standard

Runs the recommended preprocessing pipeline in order: denoise, degibbs, undistort, brain mask, smooth, rician

-n, --denoise

Denoises input DWI

--extent

Shape of denoising extent matrix, defaults to 5,5,5

--reslice

Reslices input DWI and outputs to a specific resolution in mm or output dimensions

--interp

The interpolation method to use when resizing

-g, --degibbs

Corrects Gibb’s ringing

-u, --undistort

Undistorts image using a suite of EPI distortion correction, eddy current correction, and co-registration. Does not run EPI correction if reverse phase encoding DWI is absent.

--rpe_pairs n

Speeds up topup if a reverse PE is present; specify the number (integer) of reverse PE direction B0 pairs to use

--mask

Computes a brain mask at 0.20 threshold by default

--maskthr

Specify FSL bet fractional intensity threshold for brain masking, defaults to 0.20

--user_mask

Provide path to user-generated brain mask in NifTi (.nii) format

-z, --smooth

Smooths DWI data at a default FWHM of 1.25

--fwhm

Specify the FWHM at which to smooth, defaults to 1.25

-r, --rician

Corrects Rician bias

Diffusion Tensor Control

Users may also tweak computations in estimating DTI or DKI parameters with the following flags.

--nofit

Performs preprocessing only, disables DTI/DKI parameter extraction

--noakc

Disables brute forced kurtosis tensor outlier rejection

--nooutliers

Disables IRLLS outlier detection

--fit_constraints

Specify fitting constraints to use, defaults to 0,1,0

--noqc

Disables saving of quality control (QC) metrics

--median

Performs post processing median filter of final DTI/DKI maps. WARNING: Use on a case-by-case basis for bad data only. When applied, the filter alters the values of most voxels, so it should be used with caution and avoided when data quality is otherwise adequate. While maps appear visually soother with this flag on, they may nonetheless be less accurate

Fiber Ball Imaging (FBI) Control

FBI parameters may be fine-tuned with the following flags.

--l_max n

Maximum spherical harmonic degree used in spherical harmonic expansion for fODF calculation

Pipeline Control

These are more general pipeline flags that interface directly with the user or machine.

--nthreads n

Specify number of CPU workers to use in processing, defaults to all physically available workers

--resume

Resumes preprocessing from an aborted or partial previous run

--force

Forces overwrite of existing output files

--verbose

Displays console output

--adv

Diables safety check to force run certain preprocessing steps WARNING: This flag is for advanced users only who fully understand the MRI system and its outputs. Running with this flag could potentially yield inaccuracies in resulting DTI/DKI metrics