Abstract

This research used data collected in the SOBIK study involving school aged children with Traumatic Brain Injury (TBI) and their matched controls without TBI. The purpose of this research was to analyze scans taken in the SOBIK study using a variety of neuroimaging programs to determine if there was a significant difference between the cortical thickness for these two groups of children. No significant differences were found, leading to the conclusion that cognitive functions are not necessarily affected in all patients with TBI.

Introduction

Each year, Traumatic Brain Injury (TBI) is a major contributor to neuropsychiatric morbidity and disability. For those individuals that sustain such injuries, there are three likely outcomes pertaining to the effects on cognitive functionality: full recovery, residual cognitive impairments, or dementia (Bigler, 2009, p 229). Even for those that seem to recover, there is no certainty that they will never see effects from the injury. Due to the broad nature of the definition of TBI, various types of structural damage can occur (Parikh, Koch & Narayan, 2007).  Although it is difficult to predict how future damage could occur, it is possible to scan the brains of individuals who have been affected by TBI and examine if there are consistent, significant differences in the structure of their brains. 
Using data obtained from 20 hospitalized participants, the purpose of this research is to compare the MRI scans of children 10-18 who have had traumatic brain injuries and who have not. In particular, this research will focus on the difference in cortical thickness between the two groups. If it possible to see a difference in cortical thickness for those patients who have had TBI, then it might be possible to better diagnose the cognitive changes that can occur for these patients even after they have supposedly healed.

Methods

Participants

The data I used for this paper included images from 20 participants obtained ina multi-site study in Social Outcomes of Brain Injury in Kids (SOBIK). The study had two groups of participants, both comprised of children hospitalized from injury. One group involved children who had experienced traumatic brain injury (TBI) who were matched to controls that had experienced orthopedic injury (OI). The children in the control group had not experienced any brain injury.

MRI Acquisition

The data were acquired using a 1.5T GE Signa Excite Scanner. Scans included T1-weighted images obtained using a 166-slice 3D Magnetization Prepared Rapid Gradient Echo (MPRAGE) Pulse Sequence with Repetition Time (TR) of 8.9 ms, Echo Time (TE) of 3.8 ms, flip angle of 8 degrees, Field of View (FOV) of 192 mm, 512x512 mm matrix and 1.2 mm slice thickness.

MRI Processing

All processing steps were completed on the Brigham Young University Fulton Supercomputer, a Linux system with  21,000 CPU cores across 972 compute nodes, memory per node ranging from 64-512 GB , and CPU types ranging from 6-14 core Intel (2.2-2.6 GHz).

Preprocessing

In order to improve the quality of the data analysis and remove interference from artifacts and misaligned images, the images were preprocessed using the following steps:
The images were converted from DICOM format to NifTi file format. This was done using dcm2niix (version xxx downloaded from https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage). This step makes the files readable to the programs used in later processing steps. The example code provided below exhibits a generalized form of commands used.