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Software imaging-meeting

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The document summarizes the CBS tools, which are image processing algorithms designed for high resolution brain data up to 7T. The tools are built as plug-ins for the MIPAV and JIST software and provide functions such as segmentation of cortical and sub-cortical structures, cortical surface extraction and normalization to MNI space. MIPAV is a medical image processing software developed at NIH, while JIST provides a pipeline interface and has been developed collaboratively. The tools have been tested and validated in studies comparing scan-rescan data, and are freely available online along with documentation and user support.

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Software presentation: the CBS tools for high-res brain processing up to 7T Pierre-Louis Bazin Department of Neurophysics Max Planck Institute for Human Cognitive and Brain Sciences Leipzig, Germany 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
What are the CBS Tools? High resolution image processing algorithms designed for 7T data Handles MP2RAGE data Segmentation: cortical and sub-cortical structures Cortical surface extraction and flattening (cerebral and cerebellar) Normalization to MNI space routinely at 0.4 mm Highly accurate cortical layering, profiling and thickness measurements 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
What's the software? All algorithms are built as plug-ins for the MIPAV and JIST software: Support for most medical image formats User-friendly interface Intuitive pipeline system for batch processing Integration with many additional software tools Ongoing development and support at participating institutions (NIH, MPI, JHU, Vanderbilt, ) Freely available in NITRC, NeuroDebian [McAuliffe et al., CBMS 2001] [Lucas et al., Neuroinf. 2010] 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
What is MIPAV ? A user-friendly, general medical image processing software freely available for academics, MIPAV developed at NIH MEDICAL IMAGE PROCESSING, ANALYSIS AND VISUALIZATION Advantages: read/write most medical image formats features many visualization tools (triplanar view, sequence view, 3D volume and surface rendering) many standard and advanced algorithms built-in (from image smoothing to brain stripping, or registration) full-time development team at NIH led by Dr. McAuliffe [McAuliffe et al., CBMS 2001] 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
What is JIST ? A user-friendly, pipelining interface for large data / complex processing, open source, developed at JHU, Vanderbilt, CBS, NIH Principle: LONI pipeline + MIPAV infrastructure Advantages: Inherits many MIPAV properties (file support, algorithms) many standard and advanced algorithms built-in (including DWI processing, cortical reconstruction, surface processing) Multi-processor task manager Hierarchically organized data output External tool encapsulation Command-line scripting Automated build testing Support from multiple labs [Lucas et al., Neuroinf. 2010] 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
This looks complicated ! How does it work ? 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
This looks complicated ! How does it work ? 1. Input your data 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
This looks complicated ! How does it work ? 1. Input your data 2. Press play 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
My study is complicated ! Can the software adapt ? Standard pipelines 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
My study is complicated ! Can the software adapt ? Standard pipelines Customized pipelines 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Where do I get it ? CBS High-Res Brain Tools: http://www.cbs.mpg.de/institute/software/cbs-hrt/ The latest MIPAV software available for download: http://mipav.cit.nih.gov/download/ JIST package http://www.nitrc.org/projects/JIST/ TOADS-CRUISE package http://www.nitrc.org/projects/TOADS-CRUISE/ MIPAV website NITRC website (JIST) 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
How do I learn to use it ? CBS High-Res Brain Tools: http://www.cbs.mpg.de/institute/software/cbs-hrt/documentation.html MIPAV help files: MIPAV -> Help -> Help Topics JIST documentation on NITRC: http://www.nitrc.org/plugins/mwiki/index.php/jist:MainPage Mipav help files NITRC wiki (JIST) 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Does anyone use it already ? In Neurophysics: PL Bazin J Dinse M Waehnert C Tardiff M Weiss J Schulz C Leuze R Trampel B Dhital C Stueber 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Does anyone use it already ? In Neurophysics: PL Bazin J Dinse M Waehnert C Tardiff M Weiss J Schulz C Leuze R Trampel B Dhital C Stueber In the institute: A Mestres-Miss辿 J Kipping D Margulies R Cafiero HA Jeon S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Does anyone use it already ? In Neurophysics: In other institutions: PL Bazin M McAuliffe, NIH J Dinse J Prince, JHU M Waehnert D Pham, CNRM C Tardiff B Landman, VU M Weiss J Schulz D Reich, NIH C Leuze S Resnick, NIH R Trampel P Calabresi, JHU B Dhital S Mostofski, JHU C Stueber S Ying, JHU In the institute: B Forstmann, UAmsterdam A Mestres-Miss辿 P Sch旦nknecht, ULeipzig J Kipping A Evans, MNI D Margulies S Schwarzkopf, UCL R Cafiero R Bowtell, UNottingham HA Jeon G Rees, UCL S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Does anyone use it already ? In Neurophysics: In other institutions: Current download activity PL Bazin on NITRC: M McAuliffe, NIH J Dinse J Prince, JHU M Waehnert CBS-Tools: 77 downloads D Pham, CNRM since June 2012 C Tardiff B Landman, VU M Weiss JIST: 8374 downloads J Schulz D Reich, NIH since June 2009 C Leuze S Resnick, NIH R Trampel P Calabresi, JHU B Dhital S Mostofski, JHU C Stueber S Ying, JHU In the institute: B Forstmann, UAmsterdam A Mestres-Miss辿 P Sch旦nknecht, ULeipzig J Kipping A Evans, MNI D Margulies S Schwarzkopf, UCL R Cafiero R Bowtell, UNottingham HA Jeon G Rees, UCL S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Does anyone use it already ? In Neurophysics: In other institutions: Current download activity PL Bazin on NITRC: M McAuliffe, NIH J Dinse J Prince, JHU M Waehnert CBS-Tools: 77 downloads D Pham, CNRM since June 2012 C Tardiff B Landman, VU M Weiss JIST: 8374 downloads J Schulz D Reich, NIH since June 2009 C Leuze S Resnick, NIH R Trampel P Calabresi, JHU B Dhital S Mostofski, JHU CBS support, tutorials, C Stueber S Ying, JHU troubleshooting, extensions: In the institute: PL Bazin B Forstmann, UAmsterdam A Mestres-Miss辿 P Sch旦nknecht, ULeipzig J Kipping A Evans, MNI D Margulies S Schwarzkopf, UCL R Cafiero R Bowtell, UNottingham HA Jeon G Rees, UCL S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Has it been tested and validated ? Latest results: scan-rescan experiment at 7T Freesurfer CSF cortex WM CBS tools 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Has it been tested and validated ? Main scientific publications: Waehnert, Dinse, Weiss, Streicher, Geyer, Turner & Bazin Bazin, Weiss , Dinse, Sch辰fer, Trampel, Turner Realistic Modelling of Cortical Contours A computational framework for ultra-high resolution In prep. For Neuroimage cortical analysis at 7T. In prep. For Neuroimage Landman, Bogovic, Carass, Chen, Roy, Shiee, Yang, Bazin, Ye, Bogovic, Shiee, Reich, Prince, & Pham Kishore, Pham, Bazin, Resnick & Prince. Direct segmentation of the major white matter tracts System for Integrated Neuroimaging Analysis and in diffusion tensor images. Processing of Structure. Neuroinformatics, 2012 Neuroimage, 2011. Shiee, Bazin, Ozturk, Calabresi, Reich & Pham Carass, Cuzzocreo, Wheeler, Bazin, Resnick & Prince A Topology-Preserving Approach to the Segmentation Simple paradigm for extra-cerebral tissue removal: of Brain Images with Multiple Sclerosis Lesions. Algorithm and analysis, NeuroImage, 2011 NeuroImage, 2010. Bazin & Pham Lucas, Bogovic, Carass, Bazin, Prince, Pham & Landman Homeomorphic brain image segmentation with The Java Image Science Toolkit (JIST) for Rapid topological and statistical atlases. Prototyping and Publishing of Neuroimaging Software. Medical Image Analysis, 2008. Neuroinformatics, 2010. Tosun, Rettmann, Naiman, Resnick, Kraut & Prince Han, Pham, Tosun, Rettmann, Xu & Prince Cortical Reconstruction Using Implicit Surface Evolution: CRUISE: Cortical Reconstruction Using Implicit Surface Accuracy and Precision Analysis. Evolution. NeuroImage, 2004. Neuroimage, 2005. 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
My data is at 3T, can I use it too ? Many JIST tools developed for 3T data (see Landman et al. Neuroinformatics 2012) Most 7T processing tools are 3T compatible Encapsulation of external software 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
Any other questions ? 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences

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Software imaging-meeting

  • 1. Software presentation: the CBS tools for high-res brain processing up to 7T Pierre-Louis Bazin Department of Neurophysics Max Planck Institute for Human Cognitive and Brain Sciences Leipzig, Germany 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 2. What are the CBS Tools? High resolution image processing algorithms designed for 7T data Handles MP2RAGE data Segmentation: cortical and sub-cortical structures Cortical surface extraction and flattening (cerebral and cerebellar) Normalization to MNI space routinely at 0.4 mm Highly accurate cortical layering, profiling and thickness measurements 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 3. What's the software? All algorithms are built as plug-ins for the MIPAV and JIST software: Support for most medical image formats User-friendly interface Intuitive pipeline system for batch processing Integration with many additional software tools Ongoing development and support at participating institutions (NIH, MPI, JHU, Vanderbilt, ) Freely available in NITRC, NeuroDebian [McAuliffe et al., CBMS 2001] [Lucas et al., Neuroinf. 2010] 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 4. What is MIPAV ? A user-friendly, general medical image processing software freely available for academics, MIPAV developed at NIH MEDICAL IMAGE PROCESSING, ANALYSIS AND VISUALIZATION Advantages: read/write most medical image formats features many visualization tools (triplanar view, sequence view, 3D volume and surface rendering) many standard and advanced algorithms built-in (from image smoothing to brain stripping, or registration) full-time development team at NIH led by Dr. McAuliffe [McAuliffe et al., CBMS 2001] 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 5. What is JIST ? A user-friendly, pipelining interface for large data / complex processing, open source, developed at JHU, Vanderbilt, CBS, NIH Principle: LONI pipeline + MIPAV infrastructure Advantages: Inherits many MIPAV properties (file support, algorithms) many standard and advanced algorithms built-in (including DWI processing, cortical reconstruction, surface processing) Multi-processor task manager Hierarchically organized data output External tool encapsulation Command-line scripting Automated build testing Support from multiple labs [Lucas et al., Neuroinf. 2010] 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 6. This looks complicated ! How does it work ? 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 7. This looks complicated ! How does it work ? 1. Input your data 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 8. This looks complicated ! How does it work ? 1. Input your data 2. Press play 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 9. My study is complicated ! Can the software adapt ? Standard pipelines 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 10. My study is complicated ! Can the software adapt ? Standard pipelines Customized pipelines 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 11. Where do I get it ? CBS High-Res Brain Tools: http://www.cbs.mpg.de/institute/software/cbs-hrt/ The latest MIPAV software available for download: http://mipav.cit.nih.gov/download/ JIST package http://www.nitrc.org/projects/JIST/ TOADS-CRUISE package http://www.nitrc.org/projects/TOADS-CRUISE/ MIPAV website NITRC website (JIST) 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 12. How do I learn to use it ? CBS High-Res Brain Tools: http://www.cbs.mpg.de/institute/software/cbs-hrt/documentation.html MIPAV help files: MIPAV -> Help -> Help Topics JIST documentation on NITRC: http://www.nitrc.org/plugins/mwiki/index.php/jist:MainPage Mipav help files NITRC wiki (JIST) 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 13. Does anyone use it already ? In Neurophysics: PL Bazin J Dinse M Waehnert C Tardiff M Weiss J Schulz C Leuze R Trampel B Dhital C Stueber 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 14. Does anyone use it already ? In Neurophysics: PL Bazin J Dinse M Waehnert C Tardiff M Weiss J Schulz C Leuze R Trampel B Dhital C Stueber In the institute: A Mestres-Miss辿 J Kipping D Margulies R Cafiero HA Jeon S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 15. Does anyone use it already ? In Neurophysics: In other institutions: PL Bazin M McAuliffe, NIH J Dinse J Prince, JHU M Waehnert D Pham, CNRM C Tardiff B Landman, VU M Weiss J Schulz D Reich, NIH C Leuze S Resnick, NIH R Trampel P Calabresi, JHU B Dhital S Mostofski, JHU C Stueber S Ying, JHU In the institute: B Forstmann, UAmsterdam A Mestres-Miss辿 P Sch旦nknecht, ULeipzig J Kipping A Evans, MNI D Margulies S Schwarzkopf, UCL R Cafiero R Bowtell, UNottingham HA Jeon G Rees, UCL S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 16. Does anyone use it already ? In Neurophysics: In other institutions: Current download activity PL Bazin on NITRC: M McAuliffe, NIH J Dinse J Prince, JHU M Waehnert CBS-Tools: 77 downloads D Pham, CNRM since June 2012 C Tardiff B Landman, VU M Weiss JIST: 8374 downloads J Schulz D Reich, NIH since June 2009 C Leuze S Resnick, NIH R Trampel P Calabresi, JHU B Dhital S Mostofski, JHU C Stueber S Ying, JHU In the institute: B Forstmann, UAmsterdam A Mestres-Miss辿 P Sch旦nknecht, ULeipzig J Kipping A Evans, MNI D Margulies S Schwarzkopf, UCL R Cafiero R Bowtell, UNottingham HA Jeon G Rees, UCL S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 17. Does anyone use it already ? In Neurophysics: In other institutions: Current download activity PL Bazin on NITRC: M McAuliffe, NIH J Dinse J Prince, JHU M Waehnert CBS-Tools: 77 downloads D Pham, CNRM since June 2012 C Tardiff B Landman, VU M Weiss JIST: 8374 downloads J Schulz D Reich, NIH since June 2009 C Leuze S Resnick, NIH R Trampel P Calabresi, JHU B Dhital S Mostofski, JHU CBS support, tutorials, C Stueber S Ying, JHU troubleshooting, extensions: In the institute: PL Bazin B Forstmann, UAmsterdam A Mestres-Miss辿 P Sch旦nknecht, ULeipzig J Kipping A Evans, MNI D Margulies S Schwarzkopf, UCL R Cafiero R Bowtell, UNottingham HA Jeon G Rees, UCL S Kharabian C Steele J B旦ttger 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 18. Has it been tested and validated ? Latest results: scan-rescan experiment at 7T Freesurfer CSF cortex WM CBS tools 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 19. Has it been tested and validated ? Main scientific publications: Waehnert, Dinse, Weiss, Streicher, Geyer, Turner & Bazin Bazin, Weiss , Dinse, Sch辰fer, Trampel, Turner Realistic Modelling of Cortical Contours A computational framework for ultra-high resolution In prep. For Neuroimage cortical analysis at 7T. In prep. For Neuroimage Landman, Bogovic, Carass, Chen, Roy, Shiee, Yang, Bazin, Ye, Bogovic, Shiee, Reich, Prince, & Pham Kishore, Pham, Bazin, Resnick & Prince. Direct segmentation of the major white matter tracts System for Integrated Neuroimaging Analysis and in diffusion tensor images. Processing of Structure. Neuroinformatics, 2012 Neuroimage, 2011. Shiee, Bazin, Ozturk, Calabresi, Reich & Pham Carass, Cuzzocreo, Wheeler, Bazin, Resnick & Prince A Topology-Preserving Approach to the Segmentation Simple paradigm for extra-cerebral tissue removal: of Brain Images with Multiple Sclerosis Lesions. Algorithm and analysis, NeuroImage, 2011 NeuroImage, 2010. Bazin & Pham Lucas, Bogovic, Carass, Bazin, Prince, Pham & Landman Homeomorphic brain image segmentation with The Java Image Science Toolkit (JIST) for Rapid topological and statistical atlases. Prototyping and Publishing of Neuroimaging Software. Medical Image Analysis, 2008. Neuroinformatics, 2010. Tosun, Rettmann, Naiman, Resnick, Kraut & Prince Han, Pham, Tosun, Rettmann, Xu & Prince Cortical Reconstruction Using Implicit Surface Evolution: CRUISE: Cortical Reconstruction Using Implicit Surface Accuracy and Precision Analysis. Evolution. NeuroImage, 2004. Neuroimage, 2005. 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 20. My data is at 3T, can I use it too ? Many JIST tools developed for 3T data (see Landman et al. Neuroinformatics 2012) Most 7T processing tools are 3T compatible Encapsulation of external software 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences
  • 21. Any other questions ? 10/22/12 Max Planck Institute for Human Cognitive and Brain Sciences