

Dataset input/output 

cosmo check dataset 
Check consistency of a dataset. 
cosmo fmri dataset 
load an fmri volumetric dataset 
cosmo map2fmri 
maps a dataset structure to a NIFTI, AFNI, or BV structure or file 
cosmo map2meeg 
maps a dataset to a FieldTrip or EEGlab structure or file 
cosmo map2surface 
maps a dataset structure to AFNI/SUMA NIML dset or BV SMP file 
cosmo meeg dataset 
Returns a dataset structure based on MEEG data 
cosmo surface dataset 
Returns a dataset structure based on surface mesh data 
cosmo synthetic dataset 
generate synthetic dataset 
Dataset operations 

cosmo dim insert 
insert a dataset dimension 
cosmo dim prune 
prune dataset dimension values that are not used after slicing 
cosmo dim remove 
remove a dataset dimension 
cosmo dim rename 
rename dimension attribute name 
cosmo dim transpose 
move a dataset dimension from samples to features or vice versa 
cosmo slice 
Slice a dataset by samples (the default) or features 
cosmo split 
splits a dataset by unique values in (a) sample or feature attribute(s). 
cosmo stack 
stacks multiple datasets to yield a single dataset 
Dataset processing 

cosmo average samples 
average subsets of samples by unique combinations of sample attributes 
cosmo fx 
apply a function to unique combinations of .sa or .fa values 
cosmo meeg baseline correct 
correct baseline of MEEG dataset 
cosmo normalize 
normalize dataset either by estimating or applying estimated parameters 
cosmo randomize targets 
provides randomized target labels 
cosmo remove useless data 
remove ‘useless’ (constant and/or nonfinite) samples or features 
MEEG related functions 

cosmo meeg chan neighborhood 
determine neighborhood of channels in MEEG dataset 
cosmo meeg chan neighbors 
find neighbors of MEEG channels 
cosmo meeg chantype 
return channel types and optionally a feature mask matching a type 
cosmo meeg find layout 
finds an MEEG channel layout associated with a dataset 
cosmo meeg layout collection 
return supported MEEG channel layouts 
cosmo meeg read layout 
Read FieldTrip layout 
cosmo meeg senstype2layout mapping 
return mapping from MEEG sensor types to sensor layouts 
cosmo meeg senstype collection 
return supported MEEG acquisition systems and their channel labels 
fMRI related functions 

cosmo fmri convert xform 
convert xform code between numeric and string in fmri dataset 
cosmo fmri deoblique 
deoblique a dataset 
cosmo fmri orientation 
get orientation of a dataset 
cosmo fmri reorient 
Change the orientation of an fmri dataset 
cosmo vol coordinates 
convert to and from spatial (x,y,z) coordinates 
cosmo vol grid convert 
convert between volumetric (fmri) and gridbased (meeg source) dataset 
Data visualization 

cosmo disp 
display the input as a string representation 
cosmo plot slices 
Plots a set of slices from a dataset, nifti image, or 3D data array 
Correlations 

cosmo corr 
Computes correlation  faster than than matlab’s “corr” for Pearson. 
cosmo correlation measure 
Computes a splithalf correlation measure 
Classification and crossvalidation 

cosmo classify knn 
knearest neighbor classifier 
cosmo classify lda 
linear discriminant analysis classifier  without prior 
cosmo classify libsvm 
libsvmbased SVM classifier 
cosmo classify matlabsvm 
SVM multiclassifier using matlab’s SVM implementation 
cosmo classify matlabsvm 2class 
svm classifier wrapper (around svmtrain/svmclassify) 
cosmo classify meta feature selection 
meta classifier that uses feature selection on the training data 
cosmo classify naive bayes 
naive bayes classifier 
cosmo classify nn 
nearest neighbor classifier 
cosmo classify svm 
classifier wrapper that uses either matlab’s or libsvm’s SVM. 
cosmo confusion matrix 
Returns a confusion matrix 
cosmo crossvalidate 
performs crossvalidation using a classifier 
cosmo crossvalidation measure 
performs crossvalidation using a classifier 
cosmo winner indices 
Given multiple predictions, get indices that were predicted most often. 
Representational similarity analysis 

cosmo dim generalization measure 
measure generalization across pairwise combinations over time (or any other dimension) 
cosmo dissimilarity matrix measure 
Compute a dissimilarity matrix measure 
cosmo distatis 
apply DISTATIS measure to each feature 
cosmo pdist 
compute pairwise distance between samples in a matrix 
cosmo squareform 
converts pairwise distances between matrix and vector form 
cosmo target dsm corr measure 
measure correlation with target dissimilarity matrix 
Partitioning (for crossvalidation) 

cosmo balance partitions 
balances a partition so that each target occurs equally often in each training and test chunk 
cosmo check partitions 
check whether partitions are balanced and not doubledippy 
cosmo check partitions 
check whether partitions are balanced and not doubledippy 
cosmo chunkize 
assigns chunks that are as balanced as possible based on targets. 
cosmo independent samples partitioner 
Compute partitioning scheme based on dataset with independent samples 
cosmo nchoosek partitioner 
partitions for into nchoosek(n,k) parititions with optional grouping schemas. 
cosmo nfold partitioner 
generates an nfold partition scheme 
cosmo oddeven partitioner 
generates an oddeven partition scheme 
Neighborhoods and searchlight 

cosmo cross neighborhood 
cross neighborhoods along dataset dimensions 
cosmo interval neighborhood 
compute neighborhoods stretching intervals 
cosmo meeg chan neighborhood 
determine neighborhood of channels in MEEG dataset 
cosmo naive bayes classifier searchlight 
Run (fast) Naive Bayes classifier searchlight with crossvalidation 
cosmo neighborhood split 
partitions a neighborhood in a cell with (smaller) neigborhoods 
cosmo searchlight 
Generic searchlight function returns a map of results computed at each searchlight location 
cosmo sphere offsets 
computes sub index offsets for voxels in a sphere 
cosmo spherical neighborhood 
computes neighbors for a spherical searchlight 
cosmo surficial neighborhood 
neighborhood definition for surfacebased searchlight 
Featurebased clustering 

cosmo check neighborhood 
check that a neighborhood is kosher 
cosmo cluster neighborhood 
define neighborhood suitable for clusterbased analysis 
cosmo clusterize 
fast depthfirst clustering based on equal values of neighbors 
cosmo convert neighborhood 
Converts between cell, matrix and struct representations of neighborhoods 
cosmo find local extrema 
find local extrema in a dataset using a neighborhood 
cosmo measure clusters 
General cluster measure 
cosmo montecarlo cluster stat 
compute randomeffect cluster statistics corrected for multiple comparisons 
Univariate statistics 

cosmo anova feature selector 
find the features that show the most variance between classes 
cosmo stat 
compute ttest or Ftest (ANOVA) statistic 
cosmo statcode 
Convert statcode for different analysis packages 
Utility functions 

cosmo align 
find permutation so that values in two inputs are matched 
cosmo cartprod 
returns the cartesian product with all combinations of the input 
cosmo dim find 
find dimension attribute in dataset 
cosmo dim match 
return a mask indicating match of dataset dimensions with values 
cosmo index unique 
index unique (combinations of) elements 
cosmo isequaln 
compares two input for equality with NaNs considered being equal 
cosmo isfield 
checks the presence of (possibly nested) fieldnames in a struct 
cosmo map pca 
normalize dataset either by estimating or applying estimated parameters 
cosmo mask dim intersect 
find intersection mask across a set of datasets 
cosmo match 
returns a mask indicating matching occurences in two arrays or cells relative to the second array 
cosmo overlap 
compute overlap between vectors or cellstrings in two cells 
cosmo pca 
Principal Component Analysis 
cosmo rand 
generate uniform pseudorandom numbers, optionally using a seed value 
cosmo randperm 
generate random permutation of integers 
cosmo sample unique 
sample without replacement from subsets of integers in balanced manner 
cosmo strjoin 
joins strings using a delimeter string 
cosmo strsplit 
splits a string based on another delimeter string 
cosmo structjoin 
joins values in structs or keyvalue pairs 
cosmo tail 
find values in left or right tail of a vector or string 
Misceleanous helper functions 

cosmo check external 
Checks whether a certain external toolbox exists, or list citation info 
cosmo config 
return a struc with configuration settings, or store such settings 
cosmo config 
return a struc with configuration settings, or store such settings 
cosmo dir 
list files recursively in a directory 
cosmo flatten 
flattens an arbitrary array to a dataset structure 
cosmo parallel get nproc available 
get number of processes available from Matlab parallel processing pool 
cosmo parcellfun 
applies a function to elements in a cell in parallel 
cosmo set path 
set the matlab path for CoSMoMVPA 
cosmo show progress 
Shows a progress bar, and time elapsed and expected to complete. 
cosmo type 
print or return ASCII contents of a file 
cosmo unflatten 
unflattens a dataset from 2 to (1+K) dimensions. 
cosmo warning 
show a warning message; by default just once for each message 
cosmo wizard set config 
GUIbased ‘wizard’ to set CoSMoMVPA configuration file 
Developer functions 

cosmo make temp filename 
give temporary filename that does not exist when this function is called 
cosmo notify test skipped 
notify that a test in the test suite is skipped 
cosmo publish run scripts 
helper function to publish example scripts (for developers) 
cosmo run tests 
run unit and documentation tests 
cosmo skip test if no external 
Notify that test in the test suite is skipped if no external is present 
cosmo wtf 
return system, toolbox and externals information 
Deprecated  to be removed in the future 

cosmo dataset slice fa 
Slice a dataset by features (columns) [deprecated] 
cosmo dataset slice sa 
Slice a dataset by samples (rows) [deprecated] 
cosmo dim slice 
slice and prune a dataset with dimension attributes [deprecated] 
cosmo meta feature selection classifier 
meta classifier that uses feature selection on the training data [deprecated] 
Other functions (possibly experimental) 

cosmo singleton neighborhood 
return neighborhood where each feature is only neighbor of itself 
cosmo montecarlo phase stat 
compute phase statistics based on Monte Carlo simulation 
cosmo phase itc 
compute phase inter trial coherence 
cosmo phase stat 
Compute phase perturbation, or opposition sum or product phase statistic 
cosmo tiedrank 
Compute ranks for the input along the specified dimension 
cosmo balance dataset 
subsample a dataset to have an equal number of samples for each target 
cosmo norminv 
compute inverse normal cumulative distribution function 