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