Lecture 01: Introduction

BME 234: Neuroimaging Data Analysis, Spring 2016, Course Code 14310

Frithjof Kruggel, M.D.

Department of Biomedical Engineering, University of California, Irvine
Office: REC 204, Phone: 4-3729, Email: fkruggel@uci.edu

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Syllabus
Course webpage: http://eee.uci.edu/16s/14310/
Meeting: Donald Bren Hall #1425, Tuesdays and Thursdays 2:00 PM to

3:20 PM
Office Hours: Tuesdays 1:00 PM to 2:00 PM, Thursdays 12:00 PM to
1:00 PM
Description: This course will provide the graduate student with the
knowledge and understanding of recent techniques for the analysis of
anatomical and functional neuroimaging data. Due to the interactive nature of the topic, all interested students involved in neuroimaging experiments (e.g., in Engineering, Cognitive Neuroscience, Social Sciences
and related fields) are welcome to attend. A series of lectures provides
a general introduction and overview required to understand current literature on this subject. In the second part of this course, students will
report and summarize on specific topics of the recent literature in a seminar format.
Prerequisities: Basic math, statistics and neuroanatomy
Grading: Seminar project: 70%, Discussion: 30%.
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Objectives
Participants will be able to:
identify data analysis problems typical in neuroimaging;
develop strategies for data analysis;
understand the use and limitations of specific modeling approaches;
interpret results of neuroimaging techniques;
use tools for data analysis.

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Focus
Special attention is given to:
non-invasive data acquisition methods in neuroimaging;
human studies;
the interaction of methodological and experimental approaches;
the introduction of a common terminology and ontology in this field;
cross-fertilization by mutual exchange of experience.
This course is not an introduction into:
functional neuroanatomy;
invasive methods (recording from cells or cell assemblies);
statistics or programming languages;
using SPM, AFNI, FreeSurfer (or the like).

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Web Links
Neuroanatomy: http://www9.biostr.washington.edu/
SPM Homepage: http://www.fil.ion.ucl.ac.uk/spm/
Brainvisa Homepage: http://brainvisa.info/
FreeSurfer Homepage: http://surfer.nmr.mgh.harvard.edu/
AFNI Homepage: http://afni.nimh.nih.gov/afni/
BrainLab Company Homepage: http://www.brainlab.com
Prof. Frithjof Kruggels Lab: http://sip.eng.uci.edu/
Vista image analysis SW: http://www.cs.ubc.ca/nest/lci/vista/vista.html

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Lecture Topics
Basic Neuroanatomy, MR Imaging
Registration
Segmentation
Texture Analysis
Surfaces and Volumetric Meshes
Time Series Analysis
Visualization

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Seminar
A recent journal paper will be presented by one (or more) participants.
Participants taking this course for credit are required to lead one presen

tation.
All other participants are welcome to present a paper.
Format: PPT or PDF, about 30 min, about 20 slides.
All papers and all presentations are available on the course website.
A (final) version is due one week before the seminar.
Of course: help is available!
A discussion is encouraged.
Topics: See Links on web page.

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