T2/T2* Estimation

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Calculate a \(T_2\) or \(T_2^*\) map from spin echo or gradient echo data with multiple echo times. For notational simplicitly \(T_2\) and \(T_2^*\) will be refered to as \(T_2\) below.

At least two volumes are required, however, more volumes are advised if a larger range of values are expected. For accurate results it is required that no other setting but TE varies between images.

An optional mask can also be provided to limit the calculations to a region. In addition to the \(T_2\) map, a \(S_0\) map which contains all weighting that is independent of is also produced. The parameter values are obtained by fitting the data to the signal equation

\[ S_i = S_0 e^{-TE/T_2}, i=0,1,2,\ldots,n ~~~~~~~(1) \]

where \(i\) is an index over \(n\) images with different echo times.

Inputs

Dataset

Input dataset with at least two volumes with different echo times in one or more channels of the dataset.

Type: Image, List, Required, Single

Mask

A 3D binary mask defining the region in the image where the ADC map is calculated.

Type: Mask, List, Optional, Single

Outputs

T2

The estimated T2 map.

Type: Image

S0

The estimated \(S_0\) map.

Type: Image

Settings

Configure

Algorithm Selection

Use a linearized or a nonlinear fitting model. When selecting a nonlinear model, equation (1) is fit directly with a square loss term. In the linearized case the data is transformed to yield a system of linear equations.

Values: Linear, NonLinear

Batch Size Integer

The number of voxels that are computed per batch. This is a trade-off between performance and memory consumption.

Keep Metadata Boolean

Keep or discard metadata in the parameter maps.

Configure NonLinear

Tolerance Float

The threshold change in the objective function. Changes smaller than this value imply that the fitting has converged.

Max Iterations Integer

Maximum number of iterations.

Return Convergence Map Boolean

Output a binary mask, where all true voxels have converged in the fit. This can be used to exclude voxels that did not converge.

Metadata

Echo Time Tag Text

The \(TE\)-value tag name in the metadata.

Echo Time Source Selection

Select the \(TE\)-value source for the calculation. The \(TE\)-values can be taken from the metadata, or can be supplied as an input Numeric Array.

Values: Metadata, Numeric Array Input