Lookup table of algorithm parameters

General algorithm parameters

algorParam.general.	Description
isBET	Logical value of performing brain extraction in SEPIA
fractional_threshold	Corresponding to ‘-f’ option in FSL’s BET
gradient_threshold	Corresponding to ‘-g’ option in FSL’s BET
isInvert	Use conjugate of the complex-valued data for processing
isRefineBrainMask	Exclude high R2* voxels from the edge of the brain mask

Total field recovery and phase unwrapping algorithm parameters

algorParam.unwrap.	Description
echoCombMethod	Temporal phase unwrapping method
unwrapMethod	Spatial phase unwrapping method
isEddyCorrect	Logical value of performing phase correction on data acquired with bipolar readout gradient
excludeMaskThreshold	Threshold on relative residual map to exclude unreliable voxels
excludeMethod	Method of how the unreliable voxels to be excluded
isSaveUnwrappedEcho	Logical value of saving unwrapped phase for all echoes

ROMEO (see also here)

algorParam.unwrap.	Description
offsetCorrect	corresponding to –phase-offset-correction
mask	single mask
qualitymaskThreshold	Threshold for ROMEO quality mask
useRomeoMask	Use ROMEO mask in SEPIA

Background field removal algorithm parameters

algorParam.bfr.	Description
refine_method	Method of residual B1 field removal
refine_order	Order of polynomial/spherical harmonic fitting
erode_radius	Voxel to be removed from mask edges after background field removal
erode_before_radius	Voxel to be removed from mask edges before background field removal
method	Method for background field removal

LBV

algorParam.bfr.	Description
tol	Iteration stopping criteria on the coarest grid
depth	No. of length scales
peel	No. of boundary layers to be peeled off

PDF

algorParam.bfr.	Description
tol	Iteration stopping criteria
iteration	Maximum no. of iterations allowed
padSize	Array size for zero padding

RESHARP

algorParam.bfr.	Description
radius	Radius of the spherical mean value operation
alpha	Regularisation parameter used in Tikhonov regularisation

SHARP

algorParam.bfr.	Description
radius	Radius of the spherical mean value operation
threshold	Threshold used in truncated SVD

VSHARP

algorParam.bfr.	Description
radius	Vector of radii of the spherical mean value operation in descending order

VSHARP (STI Suite)

algorParam.bfr.	Description
radius	Radius of the spherical mean value operation

iHARPERELLA

algorParam.bfr.	Description
iteration	Maximum no. of iterations allowed

QSM dipole field invevrsion algorithm parameters

algorParam.qsm.	Description
reference_tissue	Magnetic susceptibility map in ppm
method	Method for dipole field inversion

TKD

algorParam.qsm.	Description
threshold	Threshold on the dipole kernel

Closed-form solution

algorParam.qsm.	Description
lambda	Regularisation parameter used in L2-norm regularisation
optimise	Logical value of self-determination of regularisation parameter based on an L-curve approach

NDI

algorParam.qsm.	Description
tol	Iteration stopping criteria
maxiter	Maximum no. of iterations allowed
stepSize	Gradient step size of the optimizer for each iteration

STI suite iLSQR

algorParam.qsm.	Description
threshold	Threshold on the dipole kernel
maxiter	Maximum no. of iterations allowed
tol1	Iteration stopping criteria at first level
tol2	Iteration stopping criteria at second level

iLSQR

algorParam.qsm.	Description
tol	Iteration stopping criteria
maxiter	Maximum no. of iterations allowed
lambda	Regularisation parameter used in L2-norm regularisation
optimise	Logical value of self-determination of regularisation parameter based on an L-curve approach

FANSI

algorParam.qsm.	Description
tol	Iteration stopping criteria
maxiter	Maximum no. of iterations allowed
lambda	Gradient L1 penalty, regularisation weight
mu1	Gradient consistency weight
mu2	Fidelity consistency weight
solver	Linear or non-linear algorithm for dipole inversion
constraint	TV or TGV regularisation
gradient_mode	Method for regularisation spatially variable weight
isWeakHarmonic	Logical value of using weak harmonic regularisation
beta	Harmonic constrain weight
muh	Harmonic consistency weight

Star-QSM

algorParam.qsm.	Description
padsize	Array size for zero padding

MEDI

algorParam.qsm.	Description
lambda	Regularisation parameter
wData	Method of data weighting
zeropad	Array size for zero padding
percentage	Percentage of voxels considered to be edges
isSMV	Logical value of performing spherical mean value operator
radius	Radius of the spherical mean value operation
merit	Logical value of performing modal error reduction through iterative tuning
isLambdaCSF	Logical value of performing automatic zero reference (MEDI+0)
lambdaCSF	Regularisation parameter used on CSF mask

MRI Suscep. Calc.

algorParam.qsm.	Description
solver	Methods to be used for dipole field inversion
threshold	Threshold for TKD
lambda	Regularisation parameter for Tikhonov algorithms
toleance	tiolerance level for CG solver

xQSM

algorParam.qsm.	Description
solver	Pre-trained networks for dipole field inversion