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 xyz
Reslices DWI to voxel resolution specified in miliimeters (mm) or output dimensions. Performinh reslicing will skip plotting of SNR curves. Dimensions less than 9 will reslice in mm, image dimension otherwise. Specify argument as –reslice x,y,z.
- --interp CHOICE
Set the interpolation to use when reslicing. Choices are linear (default), nearest, cubic, and sinc
- -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
- -cf, --csf_fsl
Compute a CSF mask for CSF-excluded smoothing to minimize partial volume effects using FSL fit_constraints
- -cd, --csf_adc
Compute CSF mask for CSF-excluded smoothing to minimize partial volume effects by thresholding a pseudo-ADC map computed as ln(S0/S1000)/b1000. N is the ADC thresold to use (default: 2).
- -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
- -te, --multite
Enable multi-TE support. This mode preprocesses all concatenated DWIs together, but performs tensor fitting separately.
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
- --no_rectify
Disable rectification of FBI fODFs in instances where it does more harm than good. In rare instances, fODFs computed from FBI acquisitions can be degraded from rectification - this flag disables rectification for such datasets.
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