SPM8 Basics
NEXT program: October 5-7, 2009
There are no scheduled dates for this program in the future.
Its content will be incorprated into the new workshop:
"SPM8 for Basic and Clinical Investigators".
Preprocessing, experimental design and statistical analysis with SPM8
Quality assurance with various toolboxes
Visualization, anatomical labeling with various toolboxes
Curriculum Description
and Educational Objectives
Workshop Daily Schedule
Registration Information
Payment Information
Accommodations (in new window)
CURRICULUM for SPM8 Basics Workshop
Introduction: SPM8 Basics is an intermediate-level, 3-day workshop is designed for investigators having familiarity
with the fundamental principles of fMRI data acquisition and analysis.
Content: The workshop will focus on using SPM8 and its extensions for preprocessing,
statistical modeling and
visualization of data associated with a range of fMRI experimental designs. While the
primary emphasis will involve using the core SPM8 programs for these purposes, there will
also be extensive discussion of a variety
of software tools that extend the power of SPM8. Some of these tools facilitate
fMRI quality assurance through artifact detection
and mitigation at various analysis stages. Other tools support a variety of data
visualization schemes (including MRIcron, xjView,
and FreeSurfer), and will be demonstrated
interactively. We will
review and demonstrate a range of strategies for labeling cortical and subcortical regions.
Anyone planning to use SPM as their primary statistical analysis and
pre-processing software package should benefit from this program.
Users of other software packages might want to wait until there are workshops for
those packages. That said, SPM is the most widely used fMRI analysis package, and
familiarity with it in some detail would be of general benefit to anyone in this field. Moreover,
the quality control and visualization tools are applicable to most standard packages.
Participant Preparation: The workshop will involve demonstrations involving SPM8,
its extensions and associated
programs. It is necessary for participants have a means to work with this software
during the program. Therefore, participants are expected to bring a laptop with
MATLAB, SPM8 and MRIcron
already installed. Instructions for downloading these programs and others will be included in the
e-mail reply acknowledging your registration request. There may be a small number of laptops
available for use (alone or shared) by those people who cannot bring one on their own.
Please note that, although SPM itself is free and available for download from the web,
its use requires an active MATLAB license (which is not free).
The primary faculty will normally be Tom Zeffiro, Susan Whitfield-Gabrieli and Robert Savoy.
Tom and Susan have extensive experience with SPM, statistics and quality assurance
in fMRI data analysis. Robert Savoy is the director of the
fMRI Visiting Fellowship Program and
the Multi-Modal Short Course at the Martinos Center.
Educational Objectives
- Understand the basic organization of the SPM GUI
- Understand the organization of the SPM "toolbox"
- Be able to construct batch processing scripts for preprocessing and statistical modeling
- Understand the basic fMRI data preprocessing steps
- Be able to construct a preprocessing sequence including slice time correction, realignment, and spatial filtering
- Understand the origins of the artifacts most commonly encountered in fMRI datasets
- Be able to utilize explore an fMRI dataset for artifacts and effect repairs as needed
- Understand the basic fMRI single subject experimental design types
- Be able to implement statistical analysis procedures for the basic single subject fMRI designs
- Understand the basic fMRI single group experimental design types
- Be able to implement statistical analysis procedures for the basic single group fMRI designs
- Understand the basic fMRI multiple group experimental design types
- Be able to implement statistical analysis procedures for the basic multiple group fMRI designs
- Understand the process of incorporation of covariates in fMRI experimental designs
- Be able to construct and estimate statistical models involving covariates
- Be able to utilize the RIC Talairach Daemon for region labeling
- Be able to utilize the SPM Anatomy toolbox for region labeling
- Be able to utilize the FreeSurfer for region labeling
- Be able to use FreeSurfer to visualize statistical maps on the cortical surface
- Be able to use MRIcron for data visualization, including volume rendering
Lunch each day is scheduled for 90 minutes. During the last 45 minutes
of that period, there will be brief reviews or introductions to topics
for less experienced users.
