SPM12 Manual

• I Temporal processing
  • Slice Timing
    • Data
      • Session
    • Number of Slices
    • TR
    • TA
    • Slice order
    • Reference Slice
    • Filename Prefix
• II Spatial processing
  • Realign
    • Realign: Estimate
      • Data
      • Estimation Options
    • Realign: Reslice
      • Images
      • Reslice Options
    • Realign: Estimate & Reslice
      • Data
      • Estimation Options
      • Reslice Options
  • Realign & Unwarp
    • Data
      • Session
    • Estimation Options
      • Quality
      • Separation
      • Smoothing (FWHM)
      • Num Passes
      • Interpolation
      • Wrapping
      • Weighting
    • Unwarp Estimation Options
      • Basis Functions
      • Regularisation
      • Reg. Factor
      • Jacobian deformations
      • First-order effects
      • Second-order effects
      • Smoothing for unwarp (FWHM)
      • Re-estimate movement params
      • Number of Iterations
      • Taylor expansion point
    • Unwarp Reslicing Options
      • Resliced images (unwarp)?
      • Interpolation
      • Wrapping
      • Masking
      • Filename Prefix
  • Coregister
    • Coregister: Estimate
      • Reference Image
      • Source Image
      • Other Images
      • Estimation Options
    • Coregister: Reslice
      • Image Defining Space
      • Images to Reslice
      • Reslice Options
    • Coregister: Estimate & Reslice
      • Reference Image
      • Source Image
      • Other Images
      • Estimation Options
      • Reslice Options
  • Segment
    • Data
      • Channel
    • Tissues
      • Tissue
    • Warping & MRF
      • MRF Parameter
      • Clean Up
      • Warping Regularisation
      • Affine Regularisation
      • Smoothness
      • Sampling distance
      • Deformation Fields
  • Normalise
    • Normalise: Estimate
      • Data
      • Estimation Options
    • Normalise: Write
      • Data
      • Writing Options
    • Normalise: Estimate & Write
      • Data
      • Estimation Options
      • Writing Options
  • Smooth
    • Images to Smooth
    • FWHM
    • Data Type
    • Implicit masking
    • Filename Prefix
• III fMRI Statistics
  • fMRI model specification
    • Timing parameters
      • Units for design
      • Interscan interval
      • Microtime resolution
      • Microtime onset
    • Data & Design
      • Subject/Session
    • Factorial design
      • Factor
    • Basis Functions
      • Canonical HRF
      • Other basis sets
    • Model Interactions (Volterra)
    • Directory
    • Global normalisation
    • Explicit mask
    • Serial correlations
    • Reviewing your design
  • fMRI model estimation
    • Select SPM.mat
    • Method
      • Classical
      • Bayesian 1st-level
      • Bayesian 2nd-level
    • Output files
      • Classical 1st-level
      • Bayesian 1st-level
    • Model comparison
  • Factorial design specification
    • Directory
    • Design
      • One-sample t-test
      • Two-sample t-test
      • Paired t-test
      • Multiple regression
      • One-way ANOVA
      • One-way ANOVA - within subject
      • Full factorial
      • Flexible factorial
      • Partitioned model
    • Covariates
      • Covariate
    • Multiple covariates
      • Covariates
    • Masking
      • Threshold masking
      • Implicit Mask
      • Explicit Mask
    • Global calculation
      • Omit
      • User
      • Mean
    • Global normalisation
      • Overall grand mean scaling
      • Normalisation
• IV EEG/MEG
  • SPM for MEG/EEG overview
    • Welcome to SPM for M/EEG
    • Changes from SPM8 to SPM12
  • EEG/MEG preprocessing – Reference
    • Conversion of data
    • Converting arbitrary data
    • The M/EEG SPM format
    • Preparing the data after conversion and specifying batch inputs
      • Prepare (batch)
    • Integration of SPM and Fieldtrip
    • Loading data into workspace
    • The meeg object
      • Constructor meeg
      • Array-like interface
      • display
      • Number methods
      • Reading and manipulation of information
      • Reading of information
      • Manipulations of the data on disk
      • Struct-like interface
    • SPM functions
      • Epoching the data: spm_eeg_epochs
      • Filtering the data: spm_eeg_filter
      • Baseline correction: spm_eeg_bc
      • Artefact detection and rejection: spm_eeg_artefact
      • Downsampling: spm_eeg_downsample
      • Rereferencing: spm_eeg_montage
      • Grand mean: spm_eeg_grandmean
      • Merge: spm_eeg_merge
      • Multimodal fusion: spm_eeg_fuse
      • Cropping: spm_eeg_crop
      • Combine planar: spm_eeg_combineplanar
      • Data reduction: spm_eeg_reduce
      • Time-frequency decomposition: spm_eeg_tf
      • Rescaling and baseline correction of time-frequency: spm_eeg_tf_rescale
      • Averaging over time or frequency: spm_eeg_avgtime, spm_eeg_avgfreq
      • Averaging: spm_eeg_average
      • Contrast over epochs: spm_eeg_contrast
      • Copy: spm_eeg_copy
      • Remove bad trials: spm_eeg_remove_bad_trials
    • Displaying data with SPM M/EEG Review
      • Data visualization
      • Source reconstructions visualization
      • Script generation
  • Analysis in sensor space
    • Output
      • Smoothing
  • 3D source reconstruction: Imaging approach
    • Introduction
    • Getting started
    • Source space modeling
    • Coregistration
    • Forward computation (forward)
    • Inverse reconstruction
    • Summarizing the results of inverse reconstruction as an image
    • Rendering interface
    • Group inversion
    • Batching source reconstruction
    • Appendix: Data structure
  • Localization of Equivalent Current Dipoles
    • Introduction
    • Procedure in SPM12
      • Head and forward model
      • VB-ECD reconstruction
      • Result display
  • Dynamic Causal Modelling for M/EEG
    • Introduction
    • Overview
    • Calling DCM for ERP/ERF
    • load, save, select model type
    • Data and design
    • Electromagnetic model
    • Neuronal model
    • Estimation
    • Results
    • Cross-spectral densities
      • Model specification
      • The Lead-Field
      • Connections
      • Cross Spectral Densities
      • Output and Results
    • Induced responses
      • Data
      • Electromagnetic model
      • Neuronal model
      • Wavelet transform
      • Results
    • Phase-coupled responses
      • Data
      • Electromagnetic model
      • Neuronal model
      • Hilbert transform
      • Results
• V Utilities
  • Display Image
    • Image to Display
  • Check Registration
    • Images to Display
  • Rendering
    • Surface Extraction
      • Input Images
      • Surfaces
    • Surface Rendering
      • Objects
      • Lights
  • Image Calculator
    • Input Images
    • Output Filename
    • Output Directory
    • Expression
    • Additional Variables
      • Variable
    • Options
      • Data Matrix
      • Masking
      • Interpolation
      • Data Type
  • Import
    • DICOM Import
      • DICOM files
      • Output directory
      • Directory structure
      • Protocol name filter
      • Conversion options
    • MINC Import
      • MINC files
      • Options
    • ECAT Import
      • ECAT files
      • Options
    • PAR/REC Import
      • PAR files
      • Options
  • De-face Images
    • Images to de-face
  • Deformations
    • Composition
      • Dartel flow
      • Deformation Field
      • Identity (Reference Image)
      • Identity (Bounding Box and Voxel Size)
      • Imported _sn.mat
      • Inverse
    • Output
      • Save Deformation
      • Pullback
      • Pushforward
      • Surface
      • Save Jacobian Determinants
• VI Tools
  • FieldMap Toolbox
    • Introduction
    • Presubtracted Phase and Magnitude Data
      • Data
    • Real and Imaginary Data
      • Data
    • Phase and Magnitude Data
      • Data
    • Precalculated FieldMap (in Hz)
      • Data
    • Apply VDM
      • Data
      • Reslice Options
    • Creating Field Maps Using the FieldMap GUI
      • Create field map in Hz
      • Create voxel displacement map (VDM) and unwarp EPI
    • Using the FieldMap in Batch scripts
    • Using the VDM file with Unwarp
    • Appendices
      • Processing Hz field maps
      • Converting Hz field map to VDM
      • Matching field map data to EPI data
  • Dartel Tools
    • Initial Import
      • Parameter Files
      • Output Directory
      • Bounding box
      • Voxel size
      • Image option
      • Grey Matter
      • White Matter
      • CSF
    • Run Dartel (create Templates)
      • Images
      • Settings
    • Run Dartel (existing Templates)
      • Images
      • Settings
    • Normalise to MNI Space
      • Dartel Template
      • Select according to
      • Voxel sizes
      • Bounding box
      • Preserve
      • Gaussian FWHM
    • Create Warped
      • Flow fields
      • Images
      • Modulation
      • Time Steps
      • Interpolation
    • Jacobian determinants
      • Flow fields
      • Time Steps
    • Create Inverse Warped
      • Flow fields
      • Images
      • Time Steps
      • Interpolation
    • Population to ICBM Registration
      • Dartel Template
    • Kernel Utilities
      • Kernel from Images
      • Kernel from Flows
  • Shoot Tools
    • Run Shooting (create Templates)
      • Images
    • Run Shoot (existing Templates)
      • Images
      • Templates
    • Kernel Utilities
      • Kernel from velocities
      • Generate Scalar Momenta
      • Kernel from Images
  • Longitudinal Registration
    • Pairwise Longitudinal Registration
      • Time 1 Volumes
      • Time 2 Volumes
      • Time Difference
      • Noise Estimate
      • Warping Regularisation
      • Bias Regularisation
      • Save Mid-point average
      • Save Jacobian Rate
      • Save Divergence Rate
      • Deformation Fields
    • Serial Longitudinal Registration
      • Volumes
      • Times
      • Noise Estimate
      • Warping Regularisation
      • Bias Regularisation
      • Save Mid-point average
      • Save Jacobians
      • Save Divergence
      • Deformation Fields
  • Old Normalise
    • Old Normalise: Estimate
      • Data
      • Estimation Options
    • Old Normalise: Write
      • Data
      • Writing Options
    • Old Normalise: Estimate & Write
      • Data
      • Estimation Options
      • Writing Options
  • Old Segment
    • Data
    • Output Files
      • Grey Matter
      • White Matter
      • Cerebro-Spinal Fluid
      • Bias Corrected
      • Clean up any partitions
    • Custom
      • Tissue probability maps
      • Gaussians per class
      • Affine Regularisation
      • Warping Regularisation
      • Warp Frequency Cutoff
      • Bias regularisation
      • Bias FWHM
      • Sampling distance
      • Masking image
• VII Data sets and examples
  • Auditory fMRI data
    • Preamble (dummy scans)
    • Spatial pre-processing
      • Realignment
      • Coregistration
      • Segmentation
      • Normalise
      • Smoothing
    • Model specification, review and estimation
      • Estimate
    • Inference
      • Contrast manager
      • Masking
      • Thresholds
      • Files
      • Maximum Intensity Projections
      • Design matrix
      • Statistical tables
      • Plotting responses at a voxel
      • Overlays
  • Face fMRI data
    • Spatial pre-processing
      • Display
      • Realignment
      • Slice timing correction
      • Coregistration
      • Segmentation
      • Normalise
      • Smoothing
    • Modelling categorical responses
      • Estimate
      • Inference for categorical design
      • Statistical tables
      • F-contrasts
      • F-contrasts for testing effects of movement
    • Modelling parametric responses
      • Estimate
      • Plotting parametric responses
    • Bayesian analysis
      • Specification
      • Estimation
      • Inference
  • Face group fMRI data
    • Introduction
    • Data
    • Canonical HRF
    • Informed basis set
      • Nonsphericity
      • Informed Results
      • T- and F-contrasts
    • FIR basis set
      • Nonsphericity again
      • FIR Results
  • Mixed Effects Analysis
    • Introduction
  • Verbal Fluency PET data
    • Introduction
    • Single subject
    • Multiple subjects
      • Subject and Condition design
      • Subject and Time design
      • Subject by Condition design
      • Contrast manager
      • Masking and thresholds
      • MIPs and results tables
      • Small volume correction
      • Extracting data from regions
      • Inclusive Masking
      • Conjunctions
  • Dynamic Causal Modeling for fMRI
    • Theoretical background
    • Bayesian model selection
    • Practical example
      • Defining the GLM
      • Extracting time series
      • Specifying and estimating the DCM
      • Comparing models
  • Psychophysiological Interactions (PPI)
    • Theoretical background
    • Psycho-Physiologic Interaction Analysis: Summary of Steps
    • Practical example
      • GLM analysis - Design setup and estimation
      • GLM analysis - Results
    • GLM analysis - Extracting VOIs
    • PPI analysis - Create PPI variable
      • PPI GLM analysis - Design setup and estimation
      • PPI analysis - Results
      • PPI analysis - Plotting
  • Bayesian Model Inference
    • Background
    • Data
    • Analysis
      • Single Family
      • Bayesian Model Averaging
      • Family level inference
      • Summary Statistics and Group Analyses
    • BMS.mat file
      • Model level results
      • Family level results
      • Bayesian model averaging (BMA)
    • model_space.mat file
  • Dynamic Causal Modelling for resting state fMRI
    • Theoretical background
    • Practical example
      • Defining the GLM
      • Extracting time series
      • Specifying and estimating the DCM
  • MEG source localisation
    • Overview
    • Simulation
    • Imaging solutions for evoked or induced responses
      • IID (minimum norm)
      • Smooth priors (COH)
      • The Multiple sparse priors algorithm
      • Making summary images
      • Other MSP options
    • Dipole fitting to the average
      • Load/preview the data
      • Inversion
  • EEG Mismatch negativity data
    • Preprocessing
      • Simple conversion and reviewing
      • Preparing batch inputs
      • Preprocessing step by step
      • Automatisation of preprocessing
    • Sensor space analysis
      • Batching statistics
    • Source reconstruction
      • Mesh
      • Coregister
      • Forward model
      • Invert
      • Batching source reconstruction
    • Dynamic Causal Modeling
  • Advanced topics in M/EEG artefact removal
    • Artefact marking
    • Reviewing marked artefacts
    • Trial rejection based on marked artefacts
    • Explicit artefact exclusion in robust averaging
    • Topography-based artefact correction
    • Fieldtrip visual artefact rejection
  • Multimodal, Multisubject data fusion
    • Overview
    • Getting Started
    • Preprocessing M/EEG data
      • Convert (and epoch)
      • Prepare
      • Downsample
      • Baseline Correction
      • Deleting intermediate steps (optional)
      • Merging (concatenating runs)
      • Prepare (a montage for re-referencing the EEG)
      • Montage
    • Evoked analysis
      • Crop
      • Artefact detection
      • Combine Planar Gradiometers
      • Trial averaging
      • Contrasting conditions
      • Time-Sensor images
    • Scalp-Time Statistics across trials within one subject
      • Model Specification
      • Model Estimation
      • Setting up contrasts
    • Time-Frequency Analysis (Evoked and Induced power)
      • Wavelet estimation
      • Crop
      • Average
      • Baseline rescaling
      • Contrasting conditions
      • Creating 2D time-frequency images
      • Model Specification, Estimation and Contrasts
    • fMRI Preprocessing and Statistics
      • Realignment of EPI (fMRI) data
      • Normalisation/Segmentation of T1 images
      • Coregistration of mean EPI (fMRI) to T1 (sMRI)
      • Application of Normalisation parameters to EPI data
      • Smoothing
      • Creating a 1st-level (fMRI) GLM
      • Model Estimation
      • Setting up contrasts
      • Group Statistics on fMRI data
    • Source Reconstruction
      • Create Head Model
      • Model Inversion
      • Time-frequency contrasts
      • Group Statistics on Source Reconstructions
    • Group Source Reconstruction
      • Group Statistics on Source Reconstructions
    • Group MEEG Source Reconstruction with fMRI priors
      • Group Statistics on Source Reconstructions
    • References
    • Acknowledgements
  • DCM for Induced Responses
    • Data
    • Getting Started
    • Setting up DCM
      • load, save, select model type
      • Data and design
      • Electromagnetic model
    • Neuronal model
    • Estimation
    • Results
      • Frequency modes
      • Time modes
      • Time-Frequency
      • Coupling (A-Hz)
      • Coupling (B-Hz)
      • Coupling (A-modes)
      • Coupling (B-Hz)
      • Input (C-Hz)
      • Input (u-ms)
      • Dipoles
      • Save as img
    • Model comparison
  • DCM for Phase Coupling
    • Data
    • Getting Started
    • Data and design
    • Electromagnetic model
    • Neuronal model
    • Results
    • Extensions
  • DCM for Cross Spectral Densities: Anaesthesia Depth in Rodent Data
    • Overview
    • Main Results
    • Using the Graphical User Interface to Obtain those Results
      • The data
      • Dynamic Causal Modelling of Cross Spectral Densities
      • Comparing models using Bayesian Model Selection
  • DCM for fNIRS
    • Example: Motor Execution and Imagery Data
    • SPM Analysis
    • Specifying and Estimating the DCM
  • Using Dartel
    • Using Dartel for VBM
      • Using SpatialSegment
      • Using Dartel ToolsRun Dartel (create Template)
      • Using Dartel ToolsNormalise to MNI Space
    • Spatially normalising functional data to MNI space
      • An alternative approach for using Dartel to spatially normalise to MNI Space
    • Warping Images to Existing Templates
    • Warping one individual to match another
• VIII Batch Interface
  • Batch tutorial
    • Single subject
      • Study specific input data
      • Necessary processing steps
      • Add modules to the batch
      • Configure subject-independent data
      • Data flow
      • Entering subject-specific data
    • Advanced features
      • Multiple sessions
      • Processing multiple subjects in GUI
      • Command line interface
      • Modifying a saved job
  • Developer's guide
    • SPM and Matlabbatch code organisation
      • Code organisation
      • Interfaces between SPM and Matlabbatch
    • Configuration Code Details
      • Virtual Outputs
      • SPM Startup
      • Defaults Settings
    • Utilities
      • Batch Utilities
      • MATLAB Code Generation
      • Configuration Management
• IX Bibliography