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 matlabcsvm hdr

svm classifier wrapper (around fitcsvm)

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