MRI Emulator

Class: NodeMRIEmulator

Node Icon

This node is a tool for emulating magnetic resonance images for various imaging setting. It can generate contrast for spin-echo and gradient echo sequences, add realistic noise as well as simulate effects such as aliasing and fat-water-shift. Output is an image and an estimated imaging time. The node is based on the BrainWeb Phantom and two different brains datasets are available.

Figure 1: Examples of some of the images that can be created using the node.

Outputs

MR Image

Magnitude MR image.

Type: Image4DFloat

Imaging time

An estimate of the imaging time.

Type: String

Settings

Phantom

Subject Selection

Select dataset from which the MR images should be generated.

Values: Subject04, Subject05

Tissue Parameters Text

Edit the tissue specific parameter values used in the image generation.

Geometry

Settings determining the geometry of the generated image.

Matrix X Integer

Number of pixels in x-direction.

Matrix Y Integer

Number of pixels in y-direction.

Matrix Z Integer

Number of pixels in z-direction.

Resolution X [mm] Number

Resolution in x-direction, i.e. the size (in mm) of a pixel in the x-direction.

Resolution Y [mm] Number

Resolution in y-direction, i.e. the size (in mm) of a pixel in the y-direction.

Resolution Z [mm] Number

Resolution in z-direction, i.e. the size (in mm) of a pixel in the z-direction.

Position offset RL [mm] Number

Image offset in the x-direction.

Position offset AP [mm] Number

Image offset in the y-direction.

Position offset SI [mm] Number

Image offset in the y-direction.

Rotation axis RL Number

Oblique slices can be obtained by rotating the image around an axis given in three coordinates in (RL, AP, SI) directions. This setting specifies the rotation axis component in RL-direction. The rotation vector does not need to be normalized.

Rotation axis AP Number

Oblique slices can be obtained by rotating the image around an axis given in three coordinates in (RL, AP, SI) directions. This setting specifies the rotation axis component in AP-direction. The rotation vector does not need to be normalized.

Rotation axis SI Number

Oblique slices can be obtained by rotating the image around an axis given in three coordinates in (RL, AP, SI) directions. This setting specifies the rotation axis component in SI-direction. The rotation vector does not need to be normalized.

Rotation Angle [degrees] Number

The angle to rotate the image around the rotation axis. See the setting: Rotation axis RL/AP/SI.

System

System related settings, such as field strength.

Fieldstrength Selection

Select field strength of the scanner. Note that this setting only affects the SNR. To change tissue parameters such as T1 and T2 use the Tissue Parameters setting.

Values: B1_5T, B3T

Imaging coil Selection

Select imaging coil. This will impact the SNR. The IdealCoil value will produce an image with no noise.

Values: BodyCoil, HeadCoil, IdealCoil, FlexCoil

Maximum Gradient Strength [mT/m] Number

Select maximum gradient strength of the scanner. Currently this setting has no effect.

Sequence

Sequence Name Selection

Select sequence. Currently the Fast spin echo only differs from spin echo in terms of imaging time.

Values: SPGR, SE, IRSE, FSE, IRFSE

Sequence Type Selection

Select type of imaging.

Values: dim2D, dim3D

Phase endocing direction Selection

Select the phase encoding direction.

Values: dirX, dirY

Pixel bandwidth [Hz] Number

Bandwidth per pixel in Hertz.

Number of averages Number

Number of images that are averaged.

Parallel imaging factor Number

Parallel imaging acceleration factor. Affects SNR.

Use partial Fourier Boolean

Use partial Fourier to accelerate the imaging (Partial Fourier factor = 5/8).

Repetition time [ms] Number

The repetition time.

Echo time [ms] Number

The echo time.

2D settings

Slice gap [mm] Number

Slice gap in z-direction. Will not affect the resolution or image coverage. Only SNR will be affected since the effective slice thickness is decreased.

Inversion recovery settings

Inversion time [ms] Number

The inversion time.

Real reconstruction Boolean

Reconstruct real images

SPGR settings

Flip angle [deg] Number

The exitation flip angle.

References

1. http://www.bic.mni.mcgill.ca/brainweb/

2. C.A. Cocosco, V. Kollokian, R.K.-S. Kwan, A.C. Evans : "BrainWeb: Online Interface to a 3D MRI Simulated Brain Database" NeuroImage, vol.5, no.4, part 2 / 4, S425, 1997-- Proceedings of 3 - rd International Conference on Functional Mapping of the Human Brain, Copenhagen, May 1997.

3. R.K.-S. Kwan, A.C. Evans, G.B. Pike : "MRI simulation - based evaluation of image - processing and classification methods" IEEE Transactions on Medical Imaging. 18(11):1085 - 97, Nov 1999.

4. R.K.-S. Kwan, A.C. Evans, G.B. Pike : "An Extensible MRI Simulator for Post - Processing Evaluation" Visualization in Biomedical Computing(VBC'96). Lecture Notes in Computer Science, vol. 1131. Springer-Verlag, 1996. 135-140.

5. D.L. Collins, A.P. Zijdenbos, V. Kollokian, J.G. Sled, N.J. Kabani, C.J. Holmes, A.C. Evans : "Design and Construction of a Realistic Digital Brain Phantom" IEEE Transactions on Medical Imaging, vol.17, No.3, p.463--468, June 1998.

6. B. Aubert-Broche, D.L. Collins, A.C. Evans: "A new improved version of the realistic digital brain phantom" NeuroImage, in review - 2006.

7. B. Aubert-Broche, M. Griffin, G.B. Pike, A.C. Evans and D.L. Collins: "20 new digital brain phantoms for creation of validation image data bases" IEEE TMI, in review - 2006