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 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 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 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