CLEAR-SWI

Reference: Korbinian Eckstein, Beata Bachrata, Gilbert Hangel, Georg Widhalm, Christian Enzinger, Markus Barth, Siegfried Trattnig, Simon Daniel Robinson, 2021. Improved susceptibility weighted imaging at ultra-high field using bipolar multi-echo acquisition and optimized image processing: CLEAR-SWI

Pleas refer to https://github.com/korbinian90/CLEARSWI.jl to see more information regarding the options/parameters of this method.

Algorithm parameters overview

algorParam.swismwi.	Description
phaseScalingType	Shape of the phase scaling function used to build the phase mask (options: ‘tanh’, ‘negativetanh’, ‘positive’, ‘negative’, ‘triangular’)
phaseScalingStrength	Strength (contrast) of the phase scaling function applied to build the phase mask
filterSize	Size of the background high-pass filter kernel, specified as [x,y,z] in voxels
unwrappingAlgorithm	Phase unwrapping algorithm used before background removal (options: ‘laplacian’, ‘romeo’, ‘laplacianslice’)
echoCombineMethod	Method used to combine the magnitude images across echoes (options: ‘SNR’, ‘average’, ‘echo’, ‘simulated echo’)
echoCombineMethodAdd	Additional parameter required when echoCombineMethod is ‘echo’ or ‘simulated echo’ (echo number or echo time)
echoes	Echoes included in the SWI computation, specified using MATLAB indexing notation (e.g. ‘:’ for all echoes)
softplusScaling	Apply a softplus function to scale the magnitude image for improved contrast
sensitivityCorrection	Apply coil sensitivity correction to the magnitude image
ismIP	Enable minimum intensity projection (mIP) of the CLEAR-SWI image over a number of slices
slice_mIP	Number of slices used to compute the minimum intensity projection (mIP), when ismIP is enabled

Usage

algorParam.swismwi.phaseScalingType

Shape of the phase scaling function used to build the phase mask

Default Value: ‘tanh’

Examples:

algorParam.swismwi.phaseScalingType = 'tanh';

algorParam.swismwi.phaseScalingType = 'negativetanh';

algorParam.swismwi.phaseScalingType = 'triangular';

algorParam.swismwi.phaseScalingStrength

Strength (contrast) of the phase scaling function applied to build the phase mask

Default Value: 4

Examples:

algorParam.swismwi.phaseScalingStrength = 2;

algorParam.swismwi.phaseScalingStrength = 4;

algorParam.swismwi.phaseScalingStrength = 8;

algorParam.swismwi.filterSize

Size of the background high-pass filter kernel, specified as [x,y,z] in voxels

Default Value: ‘[4,4,0]’

Examples:

algorParam.swismwi.filterSize = '[2,2,0]';

algorParam.swismwi.filterSize = '[4,4,0]';

algorParam.swismwi.filterSize = '[6,6,0]';

algorParam.swismwi.unwrappingAlgorithm

Phase unwrapping algorithm used before background removal

Default Value: ‘laplacian’

Examples:

algorParam.swismwi.unwrappingAlgorithm = 'laplacian';

algorParam.swismwi.unwrappingAlgorithm = 'romeo';

algorParam.swismwi.unwrappingAlgorithm = 'laplacianslice';

algorParam.swismwi.echoCombineMethod

Method used to combine the magnitude images across echoes

Default Value: ‘SNR’

Examples:

algorParam.swismwi.echoCombineMethod = 'SNR';

algorParam.swismwi.echoCombineMethod = 'average';

algorParam.swismwi.echoCombineMethod = 'echo';

algorParam.swismwi.echoCombineMethodAdd

Additional parameter required when echoCombineMethod is ‘echo’ or ‘simulated echo’ (specifies the echo number or echo time). This field is disabled in the GUI unless echoCombineMethod is set to ‘echo’ or ‘simulated echo’.

Default Value: ‘’ (empty)

Examples:

algorParam.swismwi.echoCombineMethodAdd = '1';

algorParam.swismwi.echoCombineMethodAdd = '2';

algorParam.swismwi.echoes

Echoes included in the SWI computation, specified using MATLAB indexing notation

Default Value: ‘:’

Examples:

algorParam.swismwi.echoes = ':';

algorParam.swismwi.echoes = '1:3';

algorParam.swismwi.echoes = '2';

algorParam.swismwi.softplusScaling

Apply a softplus function to scale the magnitude image for improved contrast

Default Value: true

Examples:

algorParam.swismwi.softplusScaling = true;

algorParam.swismwi.softplusScaling = false;

algorParam.swismwi.sensitivityCorrection

Apply coil sensitivity correction to the magnitude image

Default Value: true

Examples:

algorParam.swismwi.sensitivityCorrection = true;

algorParam.swismwi.sensitivityCorrection = false;

algorParam.swismwi.ismIP

Enable minimum intensity projection (mIP) of the CLEAR-SWI image over a number of slices

Default Value: true

Examples:

algorParam.swismwi.ismIP = true;

algorParam.swismwi.ismIP = false;

algorParam.swismwi.slice_mIP

Number of slices used to compute the minimum intensity projection (mIP), when ismIP is enabled

Default Value: 4

Examples:

algorParam.swismwi.slice_mIP = 2;

algorParam.swismwi.slice_mIP = 4;

algorParam.swismwi.slice_mIP = 8;