SPM

Statistical Parametric Mapping

SPM (Statistical Parametric Mapping) refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM.

The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

SPM is made freely available to the [neuro]imaging community, to promote collaboration and a common analysis scheme across laboratories. The software represents the implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package, as a suite of MATLAB (The MathWorks, Inc) functions and subroutines with some externally compiled C routines.

Overview

• SPM website at the Wellcome Trust Centre for Neuroimaging, UCL, UK.
• Overview of SPM from Wikipedia
• Overview of SPM from Scholarpedia
• Introduction to Statistical Parametric Mapping
• History of Statistical Parametric Mapping in functional neuroimaging

Installation

Overview of SPM installation:

• Download

System Requirements (hardware and software):

• MATLAB version
• Advice on hardware selection

Detailed installation and compilation on:

• Windows
• Windows 64bit
• Linux
• Linux 64bit
• Mac OS (Intel)
• Mac OS (Intel) 64bit
• Mac OS (PowerPc)
• SunOS / Solaris

Standalone version (beta) using the MATLAB Compiler:

• Standalone SPM

Optimising your installation:

• Optimising MATLAB/SPM

Experimental Design for fMRI

• Study design and efficiency
• Block design
• Event related design

Preprocessing

• Importing data from the scanner
• DICOM Import

• Slice Timing
• Realignment
• Unwarp
• Coregistration
• Normalisation
• Segmentation
• Spatial smoothing

Statistical Inference

• F and T tests
• Correlation and Regression
• General Linear Model
• Contrasts
• Inference
• Power Analysis
• Haemodynamic Response Function
• Basis functions
• Linear Hierarchical Models
• Covariance
• Autocorrelation
• Non-sphericity
• VBM (Voxel Based Morphometry)
• Bayesian Inference
• Conjunction
• Calculating Percentage signal change
• Information to include in papers
• Results Table

Connectivity Analysis

• Introduction to connectivity
• DCM theory
• DCM practice
• The DCM Equation. 1. Motivation
• The DCM Equation. 2. Dynamical Systems
• The DCM Equation. 3. Networks and Matrices
• The DCM Equation. 4. The State Equation

Misc

• How-tos
• Programming intro
• Writing batch scripts
• Learning SPM: Courses, books and websites

Other tools

• Cogent a MATLAB-based stimulus presentation software
• MRIcron a medical images viewer
• MarsBaR region of interest toolbox for SPM
• SnPM Statistical nonParametric Mapping
• Anatomy SPM Anatomy toolbox
• AAL Anatomical Automatic Labeling
• WFU_PickAtlas a region of interest toolbox for SPM based on the Talairach Daemon Database

The physics of imaging technologies

• functional Magnetic Resonance Imaging (fMRI)
• Positron Emission Tomography (PET)
• Single Photon Emission Computed Tomography (SPECT)
• Electroencephalography (EEG)
• Magnetoencephalography (MEG)