This content refers to the previous stable release of PyMVPA. Please visit www.pymvpa.org for the most recent version of PyMVPA and its documentation.

PDF version of the PyMVPA Manual

The PDF version of the manual is available for download.

• Introduction
  • What this Manual is NOT
  • A bit of History
  • Authors & Contributors
  • How to cite PyMVPA
    • Peer-reviewed publications
    • Posters
    • Studies employing PyMVPA
  • Acknowledgements
• Installation
  • Dependencies
    • Must Have
    • Strong Recommendations
    • Suggestions
  • Installing Binary Packages
    • Debian
    • Debian backports and inofficial Ubuntu packages
    • Windows
    • MacOS X
    • RPM-based GNU/Linux Distributions
  • Building from Source
    • Three Ways to Obtain the Sources
    • Build it (General instructions)
    • Build with enabled LIBSVM bindings
    • Alternative build procedure
    • Windows
    • OpenSUSE
    • Fedora
    • MacOS X
• Getting Started
  • For the Impatient
  • Module Overview
• Datasets
  • The Basic Concepts
  • Data Mapping
  • Data Access Sugaring
  • Data Formats
  • Data Splitting
• Classifiers
  • Stateful objects
  • Error Calculation
    • Cross-validated Transfer Error
  • Error Reporting
  • Basic Supervised Learning Methods
    • Gaussian Process Regression
    • k-Nearest-Neighbour
    • Least Angle Regression
    • Penalized Logistic Regression
    • Ridge Regression
    • Sparse Multinomial Logistic Regression
    • Support Vector Machines
  • Meta-Classifiers
    • Examples of Meta-Classifiers
    • Implementation Examples
  • Retrainable Classifiers
  • Classifiers “Warehouse”
• Measures
  • Sensitivity Measures
    • Basic Sensitivity (and related Measures)
      • ANOVA
      • Linear SVM Weights
      • Other linear Classifier Weights
      • Noise Perturbation
    • Meta Sensitivity Measures
      • Splitting Measures
• Feature Selection
  • Recursive Feature Elimination
  • Incremental Feature Search
• Miscellaneous
  • Managing (Custom) Configurations
  • Progress Tracking
    • Redirecting Output
    • Verbose Messages
    • Warning Messages
    • Debug Messages
    • PyMVPA Status Summary
  • Additional Little Helpers
    • Random Number Generation
    • Unittests at a Grasp
    • Others
  • FSL Bindings
• Full Examples
  • Example fMRI Dataset
  • Preprocessing
    • Visualization of Data Projection Methods
    • Simple Data-Exploration
  • Analysis
    • Tiny Example of a Full Cross-Validation
    • Compare SMLR to Linear SVM Classifier
    • Classifier Sweep
    • The effect of different hyperparameters in GPR
    • Minimal Searchlight Example
    • Searchlight on fMRI data
    • A searchlight computing a dissimilarity matrix measure
    • Sensitivity Measure
    • Classification of SVD-mapped Datasets
    • Monte-Carlo testing of Classifier-based Analyses
    • Determine the Distribution of some Variable
    • Spatio-temporal Analysis of event-related fMRI data
  • Visualization
    • ERP/ERF-Plots
    • Simple Plotting of Classifier Behavior
    • Generating Topography plots
    • Self-organizing Maps
  • Miscellaneous
    • Kernel-Demo
    • Curve-Fitting
• PyMVPA for Matlab Users
• Frequently Asked Questions
  • General
    • It is sloooooow. What can I do?
    • I am tired of writing these endless import blocks. Any alternative?
    • I feel like I want to contribute something, do you mind?
    • I want to develop a new feature for PyMVPA. How can I do it efficiently?
    • The manual is quite insufficient. When will you improve it?
  • Data import, export and storage
    • What file formats are understood by PyMVPA?
    • What if there is no special file format for some particular datatype?
  • Data preprocessing
    • Is there an easy way to remove invariant features from a dataset?
    • How can I do block-averaging of my block-design fMRI dataset?
  • Data analysis
    • How do I know which features were finally selected by a classifier doing feature selection?
    • How do I extract sensitivities from a classifier used within a cross-validation?
    • Can PyMVPA deal with literal class labels?
• Glossary
• References
• License
• PyMVPA Development Changelog
  • Releases
• Module Reference
  • Global Facilities
    • mvpa
      • mvpa
        • Package Organization
  • Datasets: Input, Output, Storage and Preprocessing
    • datasets.base
      • Module: datasets.base
      • Dataset
    • datasets.channel
      • Module: datasets.channel
      • ChannelDataset
    • datasets.eep
      • Module: datasets.eep
      • EEPDataset
    • datasets.event
      • Module: datasets.event
      • EventDataset
    • datasets.mapped
      • Module: datasets.mapped
      • MappedDataset
    • datasets.masked
      • Module: datasets.masked
      • MaskedDataset
    • datasets.meta
      • Module: datasets.meta
      • MetaDataset
    • datasets.miscfx
      • Module: datasets.miscfx
      • Class
      • SequenceStats
      • Functions
    • datasets.miscfx_sp
      • Module: datasets.miscfx_sp
    • datasets.nifti
      • Module: datasets.nifti
      • Classes
        • ERNiftiDataset
        • NiftiDataset
      • Functions
    • datasets.splitters
      • Module: datasets.splitters
        • Module Description
        • Brief Description of Available Splitters
        • Module Organization
      • Classes
        • CustomSplitter
        • HalfSplitter
        • NFoldSplitter
        • NGroupSplitter
        • NoneSplitter
        • OddEvenSplitter
        • Splitter
  • Mappers: Data Transformations
    • mappers.array
      • Module: mappers.array
      • DenseArrayMapper
    • mappers.base
      • Module: mappers.base
      • Classes
        • ChainMapper
        • CombinedMapper
        • Mapper
        • ProjectionMapper
    • mappers.boxcar
      • Module: mappers.boxcar
      • BoxcarMapper
    • mappers.ica
      • Module: mappers.ica
      • ICAMapper
    • mappers.lle
      • Module: mappers.lle
      • LLEMapper
    • mappers.mask
      • Module: mappers.mask
      • MaskMapper
    • mappers.metric
      • Module: mappers.metric
      • Classes
        • DescreteMetric
        • Metric
    • mappers.pca
      • Module: mappers.pca
      • PCAMapper
    • mappers.procrustean
      • Module: mappers.procrustean
      • ProcrusteanMapper
    • mappers.samplegroup
      • Module: mappers.samplegroup
      • SampleGroupMapper
    • mappers.som
      • Module: mappers.som
      • SimpleSOMMapper
    • mappers.svd
      • Module: mappers.svd
      • SVDMapper
    • mappers.wavelet
      • Module: mappers.wavelet
      • Classes
        • WaveletPacketMapper
        • WaveletTransformationMapper
    • mappers.zscore
      • Module: mappers.zscore
      • ZScoreMapper
  • Classifiers and Errors
    • clfs.base
      • Module: clfs.base
      • Classes
        • Classifier
        • DegenerateInputError
        • FailedToPredictError
        • FailedToTrainError
        • LearnerError
    • clfs.blr
      • Module: clfs.blr
      • BLR
    • clfs.distance
      • Module: clfs.distance
      • Functions
    • clfs.enet
      • Module: clfs.enet
      • Classes
        • ENET
        • ENETWeights
    • clfs.glmnet
      • Module: clfs.glmnet
      • Classes
        • GLMNETWeights
        • GLMNET_C
        • GLMNET_R
    • clfs.gnb
      • Module: clfs.gnb
      • GNB
    • clfs.gpr
      • Module: clfs.gpr
      • Classes
        • GPR
        • GPRLinearWeights
    • clfs.kernel
      • Module: clfs.kernel
      • Classes
        • Kernel
        • KernelConstant
        • KernelExponential
        • KernelLinear
        • KernelMatern_3_2
        • KernelMatern_5_2
        • KernelRationalQuadratic
        • KernelSquaredExponential
    • clfs.knn
      • Module: clfs.knn
      • kNN
    • clfs.lars
      • Module: clfs.lars
      • Classes
        • LARS
        • LARSWeights
    • clfs.libsmlrc
      • Module: clfs.libsmlrc
    • clfs.libsmlrc.ctypes_helper
      • Module: clfs.libsmlrc.ctypes_helper
      • Functions
    • clfs.libsvmc.sens
      • Module: clfs.libsvmc.sens
      • LinearSVMWeights
    • clfs.libsvmc.svm
      • Module: clfs.libsvmc.svm
      • SVM
    • clfs.libsvmc.svmc
      • Module: clfs.libsvmc.svmc
      • Classes
        • svm_model
        • svm_parameter
        • svm_problem
      • Functions
    • clfs.meta
      • Module: clfs.meta
      • Classes
        • BinaryClassifier
        • BoostedClassifier
        • ClassifierCombiner
        • CombinedClassifier
        • FeatureSelectionClassifier
        • MappedClassifier
        • MaximalVote
        • MeanPrediction
        • MulticlassClassifier
        • PredictionsCombiner
        • ProxyClassifier
        • SplitClassifier
        • TreeClassifier
    • clfs.model_selector
      • Module: clfs.model_selector
      • ModelSelector
    • clfs.plr
      • Module: clfs.plr
      • PLR
    • clfs.ridge
      • Module: clfs.ridge
      • RidgeReg
    • clfs.sg.sens
      • Module: clfs.sg.sens
      • LinearSVMWeights
    • clfs.sg.svm
      • Module: clfs.sg.svm
      • SVM
    • clfs.smlr
      • Module: clfs.smlr
      • Classes
        • SMLR
        • SMLRWeights
    • clfs.stats
      • Module: clfs.stats
      • Classes
        • AdaptiveNormal
        • AdaptiveNullDist
        • AdaptiveRDist
        • FixedNullDist
        • MCNullDist
        • Nonparametric
        • NullDist
      • Functions
    • clfs.transerror
      • Module: clfs.transerror
      • Classes
        • ClassifierError
        • ConfusionBasedError
        • ConfusionMatrix
        • ROCCurve
        • RegressionStatistics
        • SummaryStatistics
        • TransferError
    • clfs.warehouse
      • Module: clfs.warehouse
      • Warehouse
  • Measures: Searchlights and Sensitivties
    • measures.anova
      • Module: measures.anova
      • Classes
        • CompoundOneWayAnova
        • OneWayAnova
    • measures.base
      • Module: measures.base
      • Classes
        • BoostedClassifierSensitivityAnalyzer
        • CombinedFeaturewiseDatasetMeasure
        • DatasetMeasure
        • FeatureSelectionClassifierSensitivityAnalyzer
        • FeaturewiseDatasetMeasure
        • MappedClassifierSensitivityAnalyzer
        • ProxyClassifierSensitivityAnalyzer
        • Sensitivity
        • SplitFeaturewiseDatasetMeasure
        • StaticDatasetMeasure
    • measures.corrcoef
      • Module: measures.corrcoef
      • CorrCoef
    • measures.corrstability
      • Module: measures.corrstability
      • CorrStability
    • measures.ds
      • Module: measures.ds
      • DSMDatasetMeasure
    • measures.glm
      • Module: measures.glm
      • GLM
    • measures.irelief
      • Module: measures.irelief
      • Classes
        • IterativeRelief
        • IterativeReliefOnline
        • IterativeReliefOnline_Devel
        • IterativeRelief_Devel
    • measures.noiseperturbation
      • Module: measures.noiseperturbation
      • NoisePerturbationSensitivity
    • measures.pls
      • Module: measures.pls
      • Classes
        • PLS
        • TaskPLS
    • measures.searchlight
      • Module: measures.searchlight
      • Searchlight
    • measures.splitmeasure
      • Module: measures.splitmeasure
      • Classes
        • SplitFeaturewiseMeasure
        • TScoredFeaturewiseMeasure
  • Feature Selection
    • featsel.base
      • Module: featsel.base
      • Classes
        • CombinedFeatureSelection
        • FeatureSelection
        • FeatureSelectionPipeline
        • SensitivityBasedFeatureSelection
    • featsel.helpers
      • Module: featsel.helpers
      • Classes
        • BestDetector
        • ElementSelector
        • FixedErrorThresholdStopCrit
        • FixedNElementTailSelector
        • FractionTailSelector
        • MultiStopCrit
        • NBackHistoryStopCrit
        • NStepsStopCrit
        • RangeElementSelector
        • StoppingCriterion
        • TailSelector
    • featsel.ifs
      • Module: featsel.ifs
      • IFS
    • featsel.rfe
      • Module: featsel.rfe
      • RFE
  • Additional Algorithms
    • algorithms.cvtranserror
      • Module: algorithms.cvtranserror
      • CrossValidatedTransferError
    • algorithms.hyperalignment
      • Module: algorithms.hyperalignment
      • Hyperalignment
  • Common Facilities
    • base
      • Module: base
        • Module Organization
      • WarningLog
    • base.config
      • Module: base.config
      • ConfigManager
    • base.dochelpers
      • Module: base.dochelpers
      • Functions
    • base.externals
      • Module: base.externals
      • Functions
    • base.info
      • Module: base.info
      • WTF
    • base.report
      • Module: base.report
      • Report
    • base.report_dummy
      • Module: base.report_dummy
      • Report
    • base.verbosity
      • Module: base.verbosity
      • Classes
        • LevelLogger
        • Logger
        • OnceLogger
        • SetLogger
  • Miscellaneous
    • misc.args
      • Module: misc.args
      • Functions
    • misc.attributes
      • Module: misc.attributes
      • Classes
        • AttributeWithUnique
        • CollectableAttribute
        • DatasetAttribute
        • FeatureAttribute
        • SampleAttribute
        • StateVariable
    • misc.bv.base
      • Module: misc.bv.base
      • BrainVoyagerRTC
    • misc.cmdline
      • Module: misc.cmdline
      • Classes
        • OptionGroups
        • Options
    • misc.data_generators
      • Module: misc.data_generators
      • Functions
    • misc.errorfx
      • Module: misc.errorfx
      • Classes
        • AUCErrorFx
        • MeanMismatchErrorFx
        • RMSErrorFx
        • RelativeRMSErrorFx
        • Variance1SVFx
      • Functions
    • misc.exceptions
      • Module: misc.exceptions
      • Classes
        • ConvergenceError
        • DatasetError
        • InvalidHyperparameterError
        • UnknownStateError
    • misc.fsl.base
      • Module: misc.fsl.base
      • Classes
        • FslEV3
        • FslGLMDesign
        • McFlirtParams
      • Function
    • misc.fsl.flobs
      • Module: misc.fsl.flobs
    • misc.fsl.melodic
      • Module: misc.fsl.melodic
      • MelodicResults
    • misc.fx
      • Module: misc.fx
      • Functions
    • misc.io.base
      • Module: misc.io.base
      • Classes
        • ColumnData
        • DataReader
        • SampleAttributes
        • SensorLocations
        • TuebingenMEGSensorLocations
        • XAVRSensorLocations
      • Functions
    • misc.io.eepbin
      • Module: misc.io.eepbin
      • EEPBin
    • misc.io.hamster
      • Module: misc.io.hamster
      • Hamster
    • misc.io.meg
      • Module: misc.io.meg
      • TuebingenMEG
    • misc.param
      • Module: misc.param
      • Classes
        • KernelParameter
        • Parameter
    • misc.plot.base
      • Module: misc.plot.base
      • Functions
    • misc.plot.erp
      • Module: misc.plot.erp
      • Functions
    • misc.plot.mri
      • Module: misc.plot.mri
    • misc.plot.topo
      • Module: misc.plot.topo
      • Functions
    • misc.state
      • Module: misc.state
      • Classes
        • AttributesCollector
        • ClassWithCollections
        • Collection
        • Harvestable
        • ParameterCollection
        • SampleAttributesCollection
        • StateCollection
    • misc.stats
      • Module: misc.stats
      • DSMatrix
    • misc.support
      • Module: misc.support
      • Classes
        • Event
        • Harvester
        • HarvesterCall
        • MapOverlap
        • SmartVersion
      • Functions
    • misc.transformers
      • Module: misc.transformers
      • Classes
        • DistPValue
        • OverAxis
      • Functions
    • misc.vproperty
      • Module: misc.vproperty
      • VProperty
    • atlases.base
      • Module: atlases.base
        • TODOs:
        • Module Organization
      • Classes
        • BaseAtlas
        • Label
        • LabelsAtlas
        • LabelsLevel
        • Level
        • PyMVPAAtlas
        • ReferencesAtlas
        • ReferencesLevel
        • XMLAtlasException
        • XMLBasedAtlas
      • Function
    • atlases.fsl
      • Module: atlases.fsl
      • Classes
        • FSLAtlas
        • FSLLabelsAtlas
        • FSLProbabilisticAtlas
    • atlases.transformation
      • Module: atlases.transformation
      • Classes
        • Linear
        • MNI2Tal_MatthewBrett
        • SpaceTransformation
        • TransformationBase
        • TypeProxy
      • Functions
    • atlases.warehouse
      • Module: atlases.warehouse