View source for 2011 Winter Project Week:Breakout Multi-Image Engineering

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Agenda breakout session: Multi-Image Engineering in slicer

Wednesday 8-10am

Session Leaders: Jim Miller, Steve Pieper, Alex Yarmakovich, Junichi Tokuda, Demian Wasserman

=Background=

Increasingly, we have data in slicer which are multi something. Examples are:
*multi-channel (T1, T2, flair, dual echo, etc.)
*DWI
*rgb and other multi-channel images
*time series

=Current State=
We have parts of the ability to handle such multi-dimensional volume in the DWI and 4D infrastructures: 

==I/O==
*Dicom to nrrd
*TimeSeriesBundleNode is a mrml node to organize 4D time series data.

==Display==
*In the volumes module, a slider allows to look at any of the individual volumes in DWI data set.
*In the 4D display module, a movie player like capability exists
*The dti infrastructure allows the display of derived scalar values such as FA and color by orientation

==Existing Processing capabilities==
Multi volumes are processed in Slicer in specialized ways. 
*Parametric analysis:
**DTI estimation from DWI
**Tofts parameter estimation from DCE
*Segmentation:
**EM segmentation from multi-channel morphology data
*Registration
**Brainsfit has in principle the ability to register multi data sets to each other and Gtract has a first solution which is engineered for DWI


=The Need=
All of the current examples are special cases. If we can generalize those into a single architecture for multi data, there would be a lot of potential for cross-benefits.
==I/O==
*We should have a single module to organize the data. DICOM to nrrd is a good start, but we need to be able to handle separate T1 and T2 acquisitions as well. We also need to be able to handle non-dicom data. Perhaps something like: load all data into slicer and associate them inside slicer in a special module. Write out as a single nrrd file.
==Display==
*we should create a single visualization infrastructure to handle multi data: compare viewers, rgb channels, time series movies: equivalent slice viewers and 3D viewers
*Compareview should allow to show multi data in compareviewers. When we have a few volumes, then we can display all. If its a large number of volumes, we will only be able to display a few. Some engineering work will be needed to make this easy on the user.
==Processing==
*common api for processing: EM segmentation, pharmacokinetic models, DWI filtering, tensor estimation should all plug into the data in the same way.