na-mic national alliance for medical image computing velocardiofacial syndrome as a genetic model...

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Velocardiofacial Syndrome as a Genetic Model for Schizophrenia

Marek KubickiDBP2, Brigham and Women’s Hospital, Harvard Medical School

National Alliance for Medical Image Computing http://na-mic.org

TeamHARVARD

• Marek Kubicki, MD, PhD• Sylvain Bouix, PhD• Yogesh Rathi, PhD• Doug Markant, BA• Usman Khan, BA

NAMIC

• Polina Golland MIT• Brad Davis Kitware• CF Westin BWH• Others


NAMIC Roadmap Project: Stochastic Tractography

Accomplished:

1. Method successfully used Stochastic Tractography with old schizophrenia data available to NAMIC (1.5T GE data) (Shenton et al., 2007).

2. Algorithm tested on smaller structures (cingulum, uncinate, arcuate, fornix). Data presented at Santa Fe in October.

3. Optimized to work with newly acquired, high resolution BWH 3T DTI data (available to NAMIC since December 2008).

4. Algorithm also tested and further debugged on phantom data (Programming week).5. New tools added to the module per our request: cutting

the tracts at the ROIs, streamline tractography option to testcontinuity of the tract.

6. Slicer3 module built (programming week).



Update- Language related connections:

1. ROIs including Brocka and Wernicke areas generated using free surfer

2. White matter masks used for tracking purposes generated also with free surfer.

3. Registration between DTI and MRI done, using demons slicer algorythm.

4. Tracts for the Arcuate Fasciculus extracted, IOFF affected by distortionsmuch more, extraction unreliable.



Outstanding related issues:

1. Distortion correction needed for the registration to be more accurate.

2. Or better registration to compensate for the distortions.

3. Measurements along the extracted tracts (automatic tract parametrization, outlier rejection?).

4. Compatibility with other data formats.


Other Projects UpdateDLPFC project

• We have been testing and improving slicer 2 DLPFC segmentation module, and optimizing segmentation for 3T structural data.

• We have been testing different bias field correction programs, in order to further fine-tune 3T slicer segmentation.

• Jim Fallon, visited PNL in Spring, and helped drawing DLPFC on all cases.

• The problem now seems to be that because the sulci are so deep, and do not run parallel to the geometric blades, we get inconsistent results. We discuss implications of the editing with Jim.


Other Contributions to the NAMIC Kit

Resting state fMRI analysis project

• We have collected resting-state fMRI data, and started analyzing it. Preliminary results have been presented at Biol Psych.

• Polina’s student (Bryce) with help from Jungsu Oh runs ICA and GMM (Gaussian Mixture Model) on the data now. Some problems with noise handling in the data…


Other Contributions to the NAMIC Kit

DTI atlas registration project

• We have obtained DTI atlas of white matter labels from MIND (Susumu Mori)

• We are trying to register these labels to our 3T DTI data through anatomical SPGR images. Preliminary data presented at Biological Psychiatry Symposium.

• We are using slicer 2, and working on improving co-registration procedures (estimating and applying deformations to different images, reverse deformations, etc). B-spline available, in the testing phase.


Collaborations within NAMIC

UNC

Corpus Callosum Subdivision using tractography-based model (Kubicki et al., paper submitted)

MIT

Whole Brain Group Spectral Clustering (new data analysis ongoing)

GaTech Cingulum Bundle analysis using Finsler method (ongoing)

Utah DTI data analysis using atlas building (ongoing)

na-mic national alliance for medical image computing velocardiofacial syndrome as a genetic model...

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