A Neuroimaging Web Interface for Data Acquisition, Processing and Visualization of Multimodal Brain Images

Authors

Gabriel M. Lizarraga, Florida International UniversityFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Computer Science

First Advisor's Name

Malek Adjouadi

First Advisor's Committee Title

committee member

Second Advisor's Name

Naphtali Rishe

Second Advisor's Committee Title

committee member

Third Advisor's Name

Giri Narasimhan

Third Advisor's Committee Title

committee member

Fourth Advisor's Name

Mercedes Cabrerizo

Fourth Advisor's Committee Title

committee member

Fifth Advisor's Name

David A Loewenstein

Fifth Advisor's Committee Title

committee member

Keywords

Biomedical, Computer and Systems Architecture, Data Storage Systems, Neurosciences

Date of Defense

10-12-2018

Abstract

Structural and functional brain images are generated as essential modalities for medical experts to learn about the different functions of the brain. These images are typically visually inspected by experts. Many software packages are available to process medical images, but they are complex and difficult to use. The software packages are also hardware intensive. As a consequence, this dissertation proposes a novel Neuroimaging Web Services Interface (NWSI) as a series of processing pipelines for a common platform to store, process, visualize and share data. The NWSI system is made up of password-protected interconnected servers accessible through a web interface. The web-interface driving the NWSI is based on Drupal, a popular open source content management system. Drupal provides a user-based platform, in which the core code for the security and design tools are updated and patched frequently. New features can be added via modules, while maintaining the core software secure and intact. The webserver architecture allows for the visualization of results and the downloading of tabulated data. Several forms are ix available to capture clinical data. The processing pipeline starts with a FreeSurfer (FS) reconstruction of T1-weighted MRI images. Subsequently, PET, DTI, and fMRI images can be uploaded. The Webserver captures uploaded images and performs essential functionalities, while processing occurs in supporting servers. The computational platform is responsive and scalable. The current pipeline for PET processing calculates all regional Standardized Uptake Value ratios (SUVRs). The FS and SUVR calculations have been validated using Alzheimer's Disease Neuroimaging Initiative (ADNI) results posted at Laboratory of Neuro Imaging (LONI). The NWSI system provides access to a calibration process through the centiloid scale, consolidating Florbetapir and Florbetaben tracers in amyloid PET images. The interface also offers onsite access to machine learning algorithms, and introduces new heat maps that augment expert visual rating of PET images. NWSI has been piloted using data and expertise from Mount Sinai Medical Center, the 1Florida Alzheimer’s Disease Research Center (ADRC), Baptist Health South Florida, Nicklaus Children's Hospital, and the University of Miami. All results were obtained using our processing servers in order to maintain data validity, consistency, and minimal processing bias.

Identifier

FIDC007047

ORCID

http://orcid.org/0000-0002-6242-6512

Recommended Citation

Lizarraga, Gabriel M., "A Neuroimaging Web Interface for Data Acquisition, Processing and Visualization of Multimodal Brain Images" (2018). FIU Electronic Theses and Dissertations. 3855.
https://digitalcommons.fiu.edu/etd/3855