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 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 |