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 |
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 |
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 |
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 |