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 montecarlo phase stat	compute phase statistics based on Monte Carlo simulation
cosmo norminv	compute inverse normal cumulative distribution function
cosmo phase itc	compute phase inter trial coherence
cosmo tiedrank	Compute ranks for the input along the specified dimension
cosmo classify matlabcsvm	svm classifier wrapper (around fitcsvm)
cosmo balance dataset	sub-sample a dataset to have an equal number of samples for each target
cosmo singleton neighborhood	return neighborhood where each feature is only neighbor of itself
cosmo phase stat	Compute phase perturbation, or opposition sum or product phase statistic