Resources

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General Image Processing

GVF Software

• 2D GVF code for Matlab is available by following this link.
• 2D Multigrid GVF code in C is available by following this link.
• 3D GVF example Java code is available here. This 3D version is built around JIST.

JIST

• The Java Image Science Toolkit (JIST) has a project page and downloads.

MGDM

• Source code and demonstrations for the Multiple-object Geometric Deformable Model (MGDM) can be found on the MGDM project page hosted by NITRC.
• A movie demo of the decomposition and evolution of MGDM.

Brain

Validation Data for Cortical Reconstruction Algorithms

• The cortical validation resource for evaluation of cortical reconstruction algorithms on both normal subjects and subjects with White Matter lesions.

Cerebellar Lobule Segmentation using Graph Cuts

• Cerebellar Lobule Segmentation Code can be used to parcellate the cerebellum into lobules given a T1w MRI image.

Subject Specific Dictionary Learning (S3DL)

• S3DL described in S. Roy, A. Carass, J.L. Prince, and D.L. Pham, "Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation", Fifth International Workshop on Machine Learning in Medical Imaging (MLMI 2014), Boston, MA, September 14, 2014. (doi) and S. Roy, Q. He, E. Sweeney, A. Carass, D.S. Reich, J.L. Prince, and D.L. Pham, "Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation", IEEE Journal of Biomedical and Health Informatics, 19(5):1598-1609, 2015. (doi)
• Software with support for segmenting lesions is available.

PET Attentuation Correction

• The PET attentuation correction method described in S. Roy, W.-T. Wang, A. Carass, J.L. Prince, J.A. Butman, and D.L. Pham, "PET Attenuation Correction Using Synthetic CT from Ultrashort Echo-Time MR Imaging", Jrnl. of Nuclear Medicine, 55:1-7, 2014. (doi)
• Matlab executables are available.

MIMECS

• MIMECS is described in: S. Roy, A. Carass, and J.L. Prince, "Magnetic Resonance Image Example Based Contrast Synthesis", IEEE Trans. on Medical Imaging, 32(12):2348-2363, 2013. (PDF) (doi)
• Code and sample data is available on our NITRC Project Page titled Image Synthesis.

Rician Mixture Model

• The Rician mixture model for segmenting the brain is described in: S. Roy, A. Carass, P.-L. Bazin, S.M. Resnick, and J.L. Prince, "Consistent Segmentation using a Rician Classifier", Medical Image Analysis, 16(2):524-535, 2012. (PDF) (doi) (PubMed)
• Matlab executables are available.

Progression Score Model

• The Progression Score Model Toolkit can be obtained from the NITRC project page.

Retinal

AURA Tools

• The AURA Tools software package allows for the automated processing and segmentation of Optical Coherence Tomography images of the macula cube. It is available from the NITRC website.

• Version 1.2 includes the software originally presented in: A. Lang, A. Carass, M. Hauser, E.S. Sotirchos, P.A. Calabresi, H.S. Ying, and J.L. Prince, "Retinal layer segmentation of macular OCT images using boundary classification", Biomedical Optics Express, 4(7):1133-1152, 2013. (PDF) (doi) (PMCID 3704094)

Cardiac

HARP

• For MATLAB demonstration software send an email to and expect a reply within five business days. We also have a collection of frequently asked questions about our HARP software.