Document Type


Date of Degree

Spring 2017

Degree Name

MS (Master of Science)

Degree In

Biomedical Engineering

First Advisor

Hans J. Johnson


Analysis of surface models reconstructed from human MR images gives re- searchers the ability to quantify the shape and size of the cerebral cortex. Increasing the reliability of automatic reconstructions would increase the precision and, therefore, power of studies utilizing cortical surface models. We looked at four different workflows for reconstructing cortical surfaces:


2) FreeSurfer + LOGISMOS-B;

3) BAW + FreeSurfer + Machine Learning + LOGISMOS-B;

4) Standard FreeSurfer(Dale et al. 1999).

Workflows 1-3 were developed in this project. Workflow 1 utilized both BRAINSAutoWorkup(BAW)(Kim et al. 2015) and a surface reconstruction tool called LOGISMOS-B(Oguz et al. 2014). Workflow 2 added LOGISMOS-B to a custom built FreeSurfer workflow that was highly optimized for parallel processing. Workflow 3 combined workflows 1 and 2 and added random forest classifiers for predicting the edges of the cerebral cortex. These predictions were then fed into LOGISMOS-B as the cost function for graph segmentation. To compare these work- flows, a dataset of 578 simulated cortical volume changes was created from 20 different sets of MR scans. The workflow utilizing machine learning (workflow 3) produced cortical volume changes with the least amount of error when compared to the known volume changes from the simulations. Machine learning can be effectively used to help reconstruct cortical surfaces that more precisely track changes in the cerebral cortex. This research could be used to increase the power of future projects studying correlations between cortical morphometrics and neurological health.


cortical reconstruction, machine learning, morphometrics, mri, random forest, surfaces


x, 62 pages


Includes bibliographical references (pages 56-62).


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Copyright © 2017 David G. Ellis