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 <https://github.com/korbinian90/ROMEO>`_)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+----------------------+--------------------------------------------+
| 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                            |
+-----------------+----------------------------------------------------------------------------+