CoSMoMVPA functions - skeleton files

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