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 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 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 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