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