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 matlabcsvm skl

svm classifier wrapper (around fitcsvm)

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 singleton neighborhood skl

return neighborhood where each feature is only neighbor of itself

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 tiedrank skl

Compute ranks for the input along the specified dimension

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