Wikibooks

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 64bit
Linux 64bit
 macOS 64bit

Instructions for older platforms: Windows

32bit, Linux 32bit, MacOS (Intel), MacOS
(PowerPc), SunOS / Solaris.

Standalone version using the MATLAB

Compiler:

Standalone SPM

Optimising your installation:

Optimising MATLAB/SPM

Containerisation:

Docker

Miscellaneous:
 GNU Octave
Continuous Integration

Experimental Design for fMRI

Design efficiency
Block design
Event related design

Data Formats
Importing data from the scanner
DICOM Import

Preprocessing
Slice Timing
Realignment
 Unwarp
Coregistration
Normalisation
Segmentation
Spatial smoothing

Modelling
Haemodynamic Response Function
Basis functions
General Linear Model
Correlation and Regression
Linear Hierarchical Models
Covariance
Autocorrelation
 Non-sphericity
Session concatenation
Group analysis

Statistical Inference
F and T tests
Contrasts
Inference
Conjunction
Power Analysis
About Correlation
Bayesian Inference
Results Table
Information to include in papers
 Calculating Percentage signal change
Comparing a single patient versus a
group of controls
Timeseries extraction

Voxel Based Morphometry

VBM (Voxel Based Morphometry)

Connectivity Analysis
Structural Equation Modelling
Psychophysiological Interactions (PPI)
Dynamic Causal Modelling (DCM)
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
Two-State DCM for fMRI
Bayesian Parameter Averaging
(BPA)
Parametric Empirical Bayes (PEB)

Misc
How-tos
Atlases
Datasets
BIDS
 Working with 4D data
Programming intro
Writing batch scripts
No Display Mode
Learning SPM: Courses, books and
websites

Other tools
Cogent a MATLAB-based stimulus
presentation software
MRIcron and MRIcroGL medical
images viewers
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
Physiological noise correction
Diffusion tools

The physics of imaging

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

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Last edited 9 months ago by SPM

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