Documentation/Nightly/Extensions/LesionSimulator

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Introduction and Acknowledgements

This work was partially funded by CAPES and CNPq, a Brazillian Agencies. Information on CAPES can be obtained on the CAPES website and CNPq website. Author: Antonio Carlos da S. Senra Filho, CSIM Laboratory (University of Sao Paulo, Department of Computing and Mathematics) Contact: Antonio Carlos da S. Senra Filho <email>acsenrafilho@usp.br</email>

CSIM Laboratory   University of Sao Paulo   CNPq Brazil   CAPES Brazil

Extension Description

This extension offer a set of tools for brain lesion simulation, based on MRI images. At moment, the module MS Lesion Simulator is available, where it can simulates both baseline scan lesion volumes (given a lesion load) and longitudinal image simulations. In summary, a statistical lesion database is generated based on a set of manual lesion mark-ups, being non-linearly registered to MNI152 space (isotropic 1mm of voxel resolution). Using a small set of parameters (lesion load, lesion homogeneity, lesion intensity indenpendence and lesion variability), it is possible to generate a broad range of MS lesions patterns in multimodal MRI imaging techniques (at moment, T1, T2, T2-FLAIR, PD, DTI-FA and DTI-ADC images are provided). For more details about this project, please see the original paper.

Modules

• MS Lesion Simulator
• MS Longitudinal Lesion Simulator

Use Cases

Most frequently used for these scenarios:

• Use Case 1: Simulate different anatomical/clinical MS lesions patterns on healthy individuals MRI images
  • In the baseline scan approach, it is offered a simulation procedure where a determined lesion load is reconstructed using a subject specific anatomical features, resulting in a realistic MS lesion load simulation.
• Use Case 2: Simulate longitudinal MS lesion progression on clinical healthy individuals MRI images

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  MS lesion simulation with 2mL lesion load

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  MS lesion simulation with 5mL lesion load

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  MS lesion simulation with 40mL lesion load

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  A 3D reconstruction of 2mL, 5mL and 40mL lesion loads showing that each lesion pattern is independent of each other

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  T1 weighted MRI brain in axial orientation (provided by the ICBM-MNI152 non linear brain template)

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  The same MNI152 template with 40mL lesion load simulated lesions (axial orientation)

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  T1 weighted MRI brain in sagittal orientation (provided by the ICBM-MNI152 non linear brain template)

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  The same MNI152 template with 40mL lesion load simulated lesions (sagittal orientation)

Similar Extensions

N/A

References

• paper

Information for Developers

Repositories:

• Source code: GitHub repository
• Issue tracker: open issues and enhancement requests