CoSMoMVPA functions

   
Dataset input/output  
cosmo check dataset Check consistency of a dataset.
cosmo fmri dataset load an fmri volumetric dataset
cosmo map2fmri maps a dataset structure to a NIFTI, AFNI, or BV structure or file
cosmo map2meeg maps a dataset to a FieldTrip or EEGlab structure or file
cosmo map2surface maps a dataset structure to AFNI/SUMA NIML dset or BV SMP file
cosmo meeg dataset Returns a dataset structure based on MEEG data
cosmo surface dataset Returns a dataset structure based on surface mesh data
cosmo synthetic dataset generate synthetic dataset
Dataset operations  
cosmo dim insert insert a dataset dimension
cosmo dim prune prune dataset dimension values that are not used after slicing
cosmo dim remove remove a dataset dimension
cosmo dim rename rename dimension attribute name
cosmo dim transpose move a dataset dimension from samples to features or vice versa
cosmo slice Slice a dataset by samples (the default) or features
cosmo split splits a dataset by unique values in (a) sample or feature attribute(s).
cosmo stack stacks multiple datasets to yield a single dataset
Dataset processing  
cosmo average samples average subsets of samples by unique combinations of sample attributes
cosmo fx apply a function to unique combinations of .sa or .fa values
cosmo meeg baseline correct correct baseline of MEEG dataset
cosmo normalize normalize dataset either by estimating or applying estimated parameters
cosmo randomize targets provides randomized target labels
cosmo remove useless data remove ‘useless’ (constant and/or non-finite) samples or features
MEEG related functions  
cosmo meeg chan neighborhood determine neighborhood of channels in MEEG dataset
cosmo meeg chan neighbors find neighbors of MEEG channels
cosmo meeg chantype return channel types and optionally a feature mask matching a type
cosmo meeg find layout finds an MEEG channel layout associated with a dataset
cosmo meeg layout collection return supported MEEG channel layouts
cosmo meeg read layout Read FieldTrip layout
cosmo meeg senstype2layout mapping return mapping from MEEG sensor types to sensor layouts
cosmo meeg senstype collection return supported MEEG acquisition systems and their channel labels
fMRI related functions  
cosmo fmri convert xform convert xform code between numeric and string in fmri dataset
cosmo fmri deoblique de-oblique a dataset
cosmo fmri orientation get orientation of a dataset
cosmo fmri reorient Change the orientation of an fmri dataset
cosmo vol coordinates convert to and from spatial (x,y,z) coordinates
cosmo vol grid convert convert between volumetric (fmri) and grid-based (meeg source) dataset
Data visualization  
cosmo disp display the input as a string representation
cosmo plot slices Plots a set of slices from a dataset, nifti image, or 3D data array
Correlations  
cosmo corr Computes correlation - faster than than matlab’s “corr” for Pearson.
cosmo correlation measure Computes a split-half correlation measure
Classification and cross-validation  
cosmo classify knn k-nearest neighbor classifier
cosmo classify lda linear discriminant analysis classifier - without prior
cosmo classify libsvm libsvm-based SVM classifier
cosmo classify matlabsvm SVM multi-classifier using matlab’s SVM implementation
cosmo classify matlabsvm 2class svm classifier wrapper (around svmtrain/svmclassify)
cosmo classify meta feature selection meta classifier that uses feature selection on the training data
cosmo classify naive bayes naive bayes classifier
cosmo classify nn nearest neighbor classifier
cosmo classify svm classifier wrapper that uses either matlab’s or libsvm’s SVM.
cosmo confusion matrix Returns a confusion matrix
cosmo crossvalidate performs cross-validation using a classifier
cosmo crossvalidation measure performs cross-validation using a classifier
cosmo winner indices Given multiple predictions, get indices that were predicted most often.
Representational similarity analysis  
cosmo dim generalization measure measure generalization across pairwise combinations over time (or any other dimension)
cosmo dissimilarity matrix measure Compute a dissimilarity matrix measure
cosmo distatis apply DISTATIS measure to each feature
cosmo pdist compute pair-wise distance between samples in a matrix
cosmo squareform converts pair-wise distances between matrix and vector form
cosmo target dsm corr measure measure correlation with target dissimilarity matrix
Partitioning (for cross-validation)  
cosmo balance partitions balances a partition so that each target occurs equally often in each training and test chunk
cosmo check partitions check whether partitions are balanced and not double-dippy
cosmo check partitions check whether partitions are balanced and not double-dippy
cosmo chunkize assigns chunks that are as balanced as possible based on targets.
cosmo independent samples partitioner Compute partitioning scheme based on dataset with independent samples
cosmo nchoosek partitioner partitions for into nchoosek(n,k) parititions with optional grouping schemas.
cosmo nfold partitioner generates an n-fold partition scheme
cosmo oddeven partitioner generates an odd-even partition scheme
Neighborhoods and searchlight  
cosmo cross neighborhood cross neighborhoods along dataset dimensions
cosmo interval neighborhood compute neighborhoods stretching intervals
cosmo meeg chan neighborhood determine neighborhood of channels in MEEG dataset
cosmo naive bayes classifier searchlight Run (fast) Naive Bayes classifier searchlight with crossvalidation
cosmo neighborhood split partitions a neighborhood in a cell with (smaller) neigborhoods
cosmo searchlight Generic searchlight function returns a map of results computed at each searchlight location
cosmo sphere offsets computes sub index offsets for voxels in a sphere
cosmo spherical neighborhood computes neighbors for a spherical searchlight
cosmo surficial neighborhood neighborhood definition for surface-based searchlight
Feature-based clustering  
cosmo check neighborhood check that a neighborhood is kosher
cosmo cluster neighborhood define neighborhood suitable for cluster-based analysis
cosmo clusterize fast depth-first clustering based on equal values of neighbors
cosmo convert neighborhood Converts between cell, matrix and struct representations of neighborhoods
cosmo find local extrema find local extrema in a dataset using a neighborhood
cosmo measure clusters General cluster measure
cosmo montecarlo cluster stat compute random-effect cluster statistics corrected for multiple comparisons
Univariate statistics  
cosmo anova feature selector find the features that show the most variance between classes
cosmo stat compute t-test or F-test (ANOVA) statistic
cosmo statcode Convert statcode for different analysis packages
Utility functions  
cosmo align find permutation so that values in two inputs are matched
cosmo cartprod returns the cartesian product with all combinations of the input
cosmo dim find find dimension attribute in dataset
cosmo dim match return a mask indicating match of dataset dimensions with values
cosmo index unique index unique (combinations of) elements
cosmo isequaln compares two input for equality with NaNs considered being equal
cosmo isfield checks the presence of (possibly nested) fieldnames in a struct
cosmo map pca normalize dataset either by estimating or applying estimated parameters
cosmo mask dim intersect find intersection mask across a set of datasets
cosmo match returns a mask indicating matching occurences in two arrays or cells relative to the second array
cosmo overlap compute overlap between vectors or cellstrings in two cells
cosmo pca Principal Component Analysis
cosmo rand generate uniform pseudo-random numbers, optionally using a seed value
cosmo randperm generate random permutation of integers
cosmo sample unique sample without replacement from subsets of integers in balanced manner
cosmo strjoin joins strings using a delimeter string
cosmo strsplit splits a string based on another delimeter string
cosmo structjoin joins values in structs or key-value pairs
cosmo tail find values in left or right tail of a vector or string
Misceleanous helper functions  
cosmo check external Checks whether a certain external toolbox exists, or list citation info
cosmo config return a struc with configuration settings, or store such settings
cosmo config return a struc with configuration settings, or store such settings
cosmo dir list files recursively in a directory
cosmo flatten flattens an arbitrary array to a dataset structure
cosmo parallel get nproc available get number of processes available from Matlab parallel processing pool
cosmo parcellfun applies a function to elements in a cell in parallel
cosmo set path set the matlab path for CoSMoMVPA
cosmo show progress Shows a progress bar, and time elapsed and expected to complete.
cosmo type print or return ASCII contents of a file
cosmo unflatten unflattens a dataset from 2 to (1+K) dimensions.
cosmo warning show a warning message; by default just once for each message
cosmo wizard set config GUI-based ‘wizard’ to set CoSMoMVPA configuration file
Developer functions  
cosmo make temp filename give temporary filename that does not exist when this function is called
cosmo notify test skipped notify that a test in the test suite is skipped
cosmo publish run scripts helper function to publish example scripts (for developers)
cosmo run tests run unit and documentation tests
cosmo skip test if no external Notify that test in the test suite is skipped if no external is present
cosmo wtf return system, toolbox and externals information
Deprecated - to be removed in the future  
cosmo dataset slice fa Slice a dataset by features (columns) [deprecated]
cosmo dataset slice sa Slice a dataset by samples (rows) [deprecated]
cosmo dim slice slice and prune a dataset with dimension attributes [deprecated]
cosmo meta feature selection classifier meta classifier that uses feature selection on the training data [deprecated]
Other functions (possibly experimental)  
cosmo balance dataset sub-sample a dataset to have an equal number of samples for each target
cosmo phase itc compute phase inter trial coherence
cosmo norminv compute inverse normal cumulative distribution function
cosmo montecarlo phase stat compute phase statistics based on Monte Carlo simulation
cosmo phase stat Compute phase perturbation, or opposition sum or product phase statistic