Difference between revisions of "Resources"

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{{h3|Cerebellar Lobule Segmentation using Graph Cuts}}
 
{{h3|Cerebellar Lobule Segmentation using Graph Cuts}}
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* The graph-cut based segmentation of the cerebellum described in {{pub|author=Z. Yang, C. Ye, J.A. Bogovic, A. Carass, B.M. Jedynak, S.H. Ying, and J.L. Prince|title=Automated Cerebellar Lobule Segmentation with Application to Cerebellar Structural Analysis in Cerebellar Disease|jrnl=ni|number=127:435-444|when=2016|doi=10.1016/j.neuroimage.2015.09.032}}
 
* {{iacl|~amod/cerlobule_seg_release_06_01_2016.tar.gz|Cerebellar Lobule Segmentation Code}} can be used to parcellate the cerebellum into lobules given a T1w MRI image.
 
* {{iacl|~amod/cerlobule_seg_release_06_01_2016.tar.gz|Cerebellar Lobule Segmentation Code}} can be used to parcellate the cerebellum into lobules given a T1w MRI image.
 +
 +
 +
{{h3|Temporal Filtering for Consistent Segmentation}}
 +
* The temporal filtering of longitudinal MR images of the brain described in {{pub|author=S. Roy, A. Carass, J. Pacheco, M. Bilgel, S.M. Resnick, J.L. Prince, and D.L. Pham|title=Temporal filtering of longitudinal brain magnetic resonance images for consistent segmentation|journal=NeuroImage: Clinical|number=11:264-275|when=2016|doi=doi:10.1016/j.nicl.2016.02.005}}
 +
* Matlab executables are {{iacl|~roy/softwares/4dfilter_Feb19-2016.zip|available}}
  
  
 
{{h3|Subject Specific Dictionary Learning (S3DL)}}
 
{{h3|Subject Specific Dictionary Learning (S3DL)}}
 
* S3DL described in {{pub|author=S. Roy, A. Carass, J.L. Prince, and D.L. Pham|title=Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation|conf=mlmi2014|doi=10.1007/978-3-319-10581-9_31|period=}} and {{pub|author=S. Roy, Q. He, E. Sweeney, A. Carass, D.S. Reich, J.L. Prince, and D.L. Pham|title=Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation|journal=IEEE Journal of Biomedical and Health Informatics|number=19(5):1598-1609|when=2015|doi=10.1109/JBHI.2015.2439242}}
 
* S3DL described in {{pub|author=S. Roy, A. Carass, J.L. Prince, and D.L. Pham|title=Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation|conf=mlmi2014|doi=10.1007/978-3-319-10581-9_31|period=}} and {{pub|author=S. Roy, Q. He, E. Sweeney, A. Carass, D.S. Reich, J.L. Prince, and D.L. Pham|title=Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation|journal=IEEE Journal of Biomedical and Health Informatics|number=19(5):1598-1609|when=2015|doi=10.1109/JBHI.2015.2439242}}
* Software with support for segmenting lesions is {{iacl|~roy/softwares/S3DL_withlesion.zip|available}}.
+
* Matlab executables are {{iacl|~roy/softwares/S3DL_withlesion.zip|available}}.
  
  
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{{h3|Rician Mixture Model}}
 
{{h3|Rician Mixture Model}}
* The Rician mixture model for segmenting the  brain is described in: {{pub|author=S. Roy, A. Carass,  P.-L. Bazin, S.M. Resnick, and J.L. Prince|title=Consistent Segmentation using a Rician Classifier|jrnl=mia|number=16(2):524-535|when=2012|doi=doi:10.1016/j.media.2011.12.001|pubmed=22204754|pdf=/proceedings/iacl/2012/RoyxMIA13-Rician_Classifier.pdf}}
+
* The Rician mixture model for segmenting the  brain is described in {{pub|author=S. Roy, A. Carass,  P.-L. Bazin, S.M. Resnick, and J.L. Prince|title=Consistent Segmentation using a Rician Classifier|jrnl=mia|number=16(2):524-535|when=2012|doi=doi:10.1016/j.media.2011.12.001|pubmed=22204754|pdf=/proceedings/iacl/2012/RoyxMIA13-Rician_Classifier.pdf}}
 
* Matlab executables are {{iacl|~roy/softwares/ricemixmodel3D.zip|available}}.
 
* Matlab executables are {{iacl|~roy/softwares/ricemixmodel3D.zip|available}}.
  

Revision as of 15:21, 18 November 2016

<meta name="title" content="Resources"/>

General Image Processing

GVF Software


JIST


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

  • The graph-cut based segmentation of the cerebellum described in Z. Yang, C. Ye, J.A. Bogovic, A. Carass, B.M. Jedynak, S.H. Ying, and J.L. Prince, "Automated Cerebellar Lobule Segmentation with Application to Cerebellar Structural Analysis in Cerebellar Disease", NeuroImage, 127:435-444, 2016. (doi)
  • Cerebellar Lobule Segmentation Code can be used to parcellate the cerebellum into lobules given a T1w MRI image.


Temporal Filtering for Consistent Segmentation

  • The temporal filtering of longitudinal MR images of the brain described in S. Roy, A. Carass, J. Pacheco, M. Bilgel, S.M. Resnick, J.L. Prince, and D.L. Pham, "Temporal filtering of longitudinal brain magnetic resonance images for consistent segmentation", NeuroImage: Clinical, 11:264-275, 2016. (doi)
  • Matlab executables are available


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)
  • Matlab executables are available.


PET Attentuation Correction


MIMECS


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


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.


Cardiac

HARP

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