CoSMoMVPA functions - header signature files

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