MRI Emulator

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Emulates images produced by MRI scanners for some common sequences. The emulation uses signal equations and add some common effects. This the emulatated images corresponds to “ideal” outputs of a scanners.

Effects that are simulated:

Noise
Aliasing
Fat-water shift and phase effects.

In addition to producing emulated MRI images, the node can also output tissue maps and parameter maps (T1, T2 etc).

Outputs

Output

The emulated images or tissues/tissue paramters if one of those output options is selected.

Type: NodeIOImage

Settings

Phantom

Name Selection

Select the phantom to be used in the simulation.

Values: Brainweb 4, Brainweb 5

Geometry

Specification Selection

Select how the geometry should be specified. The region to be imaged and its resolution can be defined using a field-of-view, an acquisition matrix and a voxel size. Two of these will imply the third one. This setting defines which two that you specify.

Values: Matrix + Field of View, Matrix + Voxel Size, Field of View + Voxel Size

Position [mm]Numbers

Position of the iso-center relative to the center of the phantom. Units in mm.

Acquisition Matrix Integers

The size of the data acquisition matrix.

Field Of View [mm] Numbers

The size of the imaged field-of-view in mm.

VoxelSize [mm]Numbers

The size of the voxels in mm.

Slice Gap [mm]Float

Gap between slices in mm. Valid for 2D sequences only.

Orientation Axis Numbers

The imaging field of view is rotated around the iso-center along this axis by and angle specified by the Orientation Angle setting. The axis does not need to be normalized to length 1.

Orientation Angle [degrees]Float

Rotation angle for the imaging field-of-view in degrees.

Sequence

Sequence Name Selection

The MRI sequence to be emulated. The following sequnces with associated signal equations can be emulated:

Spoiled Gradient Echo

$$s = \frac{\rho(1-e^{-TR/T1})\sin(\theta)e^{-TE/T2^*}}{1-\cos(\theta)e^{-TR/T1}} $$

Spin Echo

\[ \begin{aligned} &s = \rho (1+ \Delta(\alpha)- e^{-(TR-TE/2)/T1})e^{-TE/T2}\sin^2(\alpha) \\ &\Delta(\alpha) = \cos(\alpha)e^{-TR/T1}(e^{TE/(2\cdot T1)}-1) \end{aligned} \]

Inversion Recovery Spin Echo

\[ \begin{aligned} &s = \rho (M_z \cos(\beta)e^{-TI/T1} + 1 - e^{-TI/T1})e^{-TE/T2}\sin^2(\alpha) \\ &M_z = 1+ \Delta(\alpha)- e^{-(TR-TE/2)/T1} \\ &\Delta(\alpha) = \cos(\alpha)e^{-TR/T1}(e^{TE/(2\cdot T1)}-1) \end{aligned} \]

Turbo Spin Echo The same equation as for Spin Echo is used.
Inversion Recovery Turbo Spin Echo The same equation as for Inversion Recovery Spin Echo is used.

Where $\alpha$ is the refocusing flip angle and $\beta$ is the inversion flip angle. The excitation flip angle is be $90^o$.

Values: Spoiled Gradient Echo, Spin Echo, Turbo Spin Echo, Inversion Recovery Spin Echo, Inversion Recovery Turbo Spin Echo

Sequence Type Selection

The type of dimensionallity of for the sequence (2D or 3D).

Values: 2D, 3D

Phase Encoding Direction Selection

Direction of the phase encoding.

Values: i, j

Reconstruction Selection

How the image should be reconstructed.

Values: Magnitude, Real, Complex

Bandwidth Per Pixel [Hz]Float

Receiver bandwidth per pixel in Hz.

Number Of Averages Integer

Number of signal averages used. Will affect the noise.

Turbo Factor Integer

Number of echoes per excitation used with Turbo spin-echo sequences. Will affect the simulated time it takes to acquire an image.

Partial Fourier Factor Float

Partial Fourier factor used. Set to one if not used. Will affect the noise.

Parallel Imaging Factor Integer

Parallel imaging factor used. Set to one if not used. Will affect the noise.

Contrast

Repetition Time [mm]Float

The repetition time for the sequence in ms.

Echo Time [mm]Float

The echo time for the sequence in ms.

Inversion Time [mm]Float

The inversion time for the sequence in ms.

Flip Angle [mm]Float

Excitation flip angle in degrees.

Refocusing Flip Angle [degrees]Float

Refocusing flip angle in degrees.

Inversion Flip Angle [degrees]Float

Inversion flip angle in degrees.

System

Output Selection

Resulting output from the node.

Emulation: Emulates an MRI scanner.
Tissue Parameters: Creates maps of tissue parameters such as T1 and T2.
Tissue Types: Creates maps of tissue types. For example gray and white matter maps.

Values: Emulation, Tissue Parameters, Tissue Types

Field Strength Selection

Fieldstrength of the scanner. Will affect contrast and noise.

Values: 1.5 T, 3 T

Coil Selection

Type of coil used. The Head, Flexible and Body coils have noise levels that mimic those of a real scanner using:

Head Coil: A coil dedicated to head imaging.
Flex Coil: A flexible array coil that can be placed on the subjects body.
Body Coil: The built-in coil in the scanner bore.

The Ideal Coil coil adds no noise. The Select SNR adds a user-defined amount of noise that results in a fix noise indepentent of imaging settings. The resulting standard deviation of the noise when this setting is used is $1/SNR$.

Values: Head Coil, Flex Coil, Body Coil, Ideal Coil, Select SNR

SNR Float

The relative SNR to be simulated when the Select SNR option is used for the Coil setting. A value of 1 implies the same SNR as for the Head coil.

Maximum Gradient Strength [mT/m]Float

The maximum gradient strength of the system in mT/m. Will affect the imaging time as well as minimum values of e.g. Repetition Time and Echo Time.

Slew Rate [T/m/s]Float

The maximum gradient slew-rate of the system in T/m/s. Will affect the imaging time as well as minimum values of e.g. Repetition Time and Echo Time.