Ryan Cabeen: Created page with "Deriving connectivity information from diffusion MRI has become a standard approach for understanding brain anatomy. We are currently developing tools to generate brain conne..."

2012-04-05T16:23:47Z

Created page with "Deriving connectivity information from diffusion MRI has become a standard approach for understanding brain anatomy. We are currently developing tools to generate brain conne..."

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Deriving connectivity information from diffusion MRI has become a standard approach for understanding brain anatomy. We are currently developing tools to generate brain connectivity networks, but one technical challenge is how the networks are represented. This mostly affects the exchange of data between tools that generate and process the networks, tools for visualizations, and tools for statistical analysis. This page outlines some of the technical concerns for dealing with these networks.

==Requirements==

'''Multiple networks'''
* hundreds to thousands of subjects
* would like to compare in visualizations

'''Node attributes'''
* names of regions of interest
* several numerical anatomical measures

'''Edge attributes'''
* names of intersecting tracts
* a few dozen numerical anatomical measures

==File Formats==

{| class="wikitable" style="text-align: center;"
|'''Name'''
|'''Pros'''
|'''Cons'''
|'''Support'''
|-
|[http://en.wikipedia.org/wiki/Comma-separated_values CSV]
|Simple to parse, unix friendly
|Can't effectively handle multiple networks, many flavors
|Excel, [http://www.paraview.org/ Paraview], [http://www.cytoscape.org Cytoscape]
|-
|[http://graphml.graphdrawing.org/ GraphML]
|Flexible, rich features
|Supports more features than necessary, larger file size
|[http://gephi.org/ Gephi], [http://prefuse.org/ prefuse]
|-
|[http://cmtk.org/cfflib CML]
|Plays well with other connectome software
|Doesn't play well with anything else
|[http://connectomeviewer.org/viewer Connectome Viewer]
|-
|[http://nifti.nimh.nih.gov/nifti-1/ NIfTi]
|Good for comparing multiple networks
|A hack. Doesn't store node names
|[http://www.fmrib.ox.ac.uk/fsl/fslview/index.html FSLView] and others
|}

==References==

[http://umcd.humanconnectomeproject.org/ UCLA Multimodal Connectivity Database]

[http://www.humanconnectome.org/ Human Connectome]

[http://www.humanconnectomeproject.org/ Human Connectome Project]

[http://openconnecto.me/ Open Connectome]

[http://www.connectomeviewer.org/ Connectome Viewer]

[http://www.cmtk.org/ Connectome Mapping Toolkit]

[http://nipy.sourceforge.net/ NiPy]

Brain Networks - Revision history

Ryan Cabeen: Created page with "Deriving connectivity information from diffusion MRI has become a standard approach for understanding brain anatomy. We are currently developing tools to generate brain conne..."