Software imaging-meeting

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


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]

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]


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]


This looks complicated ! How does it work ?


1. Input your data


1. Input your data

2. Press play


My study is complicated ! Can the software adapt ?

Standard pipelines


My study is complicated ! Can the software adapt ?

Standard pipelines

Customized pipelines

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)


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)

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 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-Missé
J Kipping
D Margulies
R Cafiero
HA Jeon
S Kharabian
C Steele
J Böttger


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-Missé P Schönknecht, 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 Böttger


In Neurophysics: In other institutions: Current download activity
PL Bazin on NITRC:
M McAuliffe, NIH
M Waehnert CBS-Tools: 77 downloads
D Pham, CNRM since June 2012
M Weiss JIST: 8374 downloads
J Schulz D Reich, NIH since June 2009
B Dhital S Mostofski, JHU
C Stueber S Ying, JHU

In the institute:
HA Jeon G Rees, UCL
S Kharabian
C Steele
J Böttger


In Neurophysics: In other institutions: Current download activity
PL Bazin on NITRC:
M McAuliffe, NIH
M Waehnert CBS-Tools: 77 downloads
D Pham, CNRM since June 2012
M Weiss JIST: 8374 downloads
J Schulz D Reich, NIH since June 2009
B Dhital S Mostofski, JHU CBS support, tutorials,
C Stueber S Ying, JHU troubleshooting, extensions:
In the institute: PL Bazin
HA Jeon G Rees, UCL
S Kharabian
C Steele
J Böttger


Has it been tested and validated ?
Latest results: scan-rescan experiment at 7T

Freesurfer

CSF cortex WM
CBS tools


Has it been tested and validated ?
Main scientific publications:

Waehnert, Dinse, Weiss, Streicher, Geyer, Turner & Bazin Bazin, Weiss , Dinse, Schäfer, 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.


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


Any other questions ?


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