View source for Clinically oriented structural, connectomic and functional analysis of traumatic brain injury in 3D Slicer

==Key Investigators==
Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig

Whereas our previously developed workflows for TBI longitudinal data analysis in 3D Slicer have been very useful for the analysis of severe TBI with large lesion loads, we have not yet investigated how robust our algorithms and methodologies are for the purpose of analyzing mild TBI data as well as data from TBI cases with low to moderate lesion loads. The purpose of this project is to work with our collaborators at the University of Utah and at Kitware in order to identify and solve the challenges posed by the application of TBI analysis algorithms to low- to moderate-load TBI cases. 

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<h3>Objective</h3>
* Develop 3D Slicer workflows dedicated to the analysis of multimodal MRI data from TBI cases with low to moderate lesion loads. 
* Identify optimal ways to use algorithms developed by the Utah and Kitware teams so that these algorithms can accommodate data sets which exhibit varying degrees of lesion extent
* Interact with our collaborators to determine how best to use their TBI pathology detection algorithms so that clinicians can use these methods with improved sensitivity and specificity with respect to the detection of lesions which are minor or otherwise difficult to detect via MRI
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<h3>Approach, Plan</h3>
* co-registration of DTI and MRI data will be performed in 3D Slicer to identify optimal workflows for data analysis
* Multimodal MRI cases of TBI patients will be reviewed and analyzed with a focus on determining and improving the sensitivity threshold of pathology detection algorithms developed by our collaborators in Utah and North Carolina. 
* DTI data will be analyzed to determine what connectivity changes occur longitudinally in the TBI brain
* the complex relationship between pathology-related hypo- and hyperintensities in MRI and connectomic abnormalities as revealed by DTI will be investigated and new methods will be developed for studying such relationships
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<h3>Progress</h3>
* We have formulated an approach to the registration of DTI volumes to anatomic T1 volumes in TBI
* We evaluated the potential to use 3D Slicer for reduction of susceptibility artifacts in DTI scans of TBI
* Our activities have included a review of how network theory can be used to identify clinical outcome biomarkers in 3D Slicer based on DTI volume data
* We developed and discussed a framework for using 3D Slicer to perform structural and functional connectomic analysis based on multimodal MRI, fMRI and EEG neuroimaging
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