Index

A

Absolute() (in module mvpa2.misc.transformers) ACTIONS (mvpa2.misc.cmdline.Option attribute) add() (mvpa2.misc.cmdline.OptionGroups method) add_option_group() (mvpa2.misc.cmdline.OptionParser method) AFNI alternative build procedure ALWAYS_TYPED_ACTIONS (mvpa2.misc.cmdline.Option attribute) API reference

array() (in module mvpa2.misc.neighborhood) array_whereequal() (in module mvpa2.misc.support) as_descrete_time() (mvpa2.misc.support.Event method) Atlas() (in module mvpa2.atlases) AttributeMap (class in mvpa2.misc.attrmap) ATTRS (mvpa2.misc.cmdline.Option attribute) auc_error() (in module mvpa2.misc.errorfx) autocorrelated_noise() (in module mvpa2.misc.data_generators)

B

backports between-subject classification, [1] binary packages, [1] Block-averaging, [1] borrowdoc() (in module mvpa2.misc.neighborhood)

borrowkwargs() (in module mvpa2.misc.neighborhood) build instructions building from source building on Windows

C

C (mvpa2.misc.data_generators.Dataset attribute) CachedQueryEngine (class in mvpa2.misc.neighborhood) cartesian_distance() (in module mvpa2.misc.neighborhood) cfg changelog CHECK_METHODS (mvpa2.misc.cmdline.Option attribute) check_value() (mvpa2.misc.cmdline.Option method) check_values() (mvpa2.misc.cmdline.OptionParser method) chirp_linear() (in module mvpa2.misc.data_generators) chisquare() (in module mvpa2.misc.stats) Chunk chunks (mvpa2.misc.data_generators.Dataset attribute) citation Classifier ClassWithCollections (class in mvpa2.misc.transformers)

clear() (mvpa2.misc.attrmap.AttributeMap method) code swarm Conditional Attribute ConditionalAttribute (class in mvpa2.misc.transformers) config file configuration Confusion Matrix CONST_ACTIONS (mvpa2.misc.cmdline.Option attribute) convert_value() (mvpa2.misc.cmdline.Option method) copy() (in module mvpa2.misc.support) corr_error() (in module mvpa2.misc.errorfx) corr_error_prob() (in module mvpa2.misc.errorfx) correlation() (in module mvpa2.misc.errorfx) cross-validation, [1], [2], [3] Cross-validation, [1], [2]

D

Dataset (class in mvpa2.misc.data_generators) Dataset attribute Dataset concepts Dataset Database Debian, [1] debug, [1] Decoding deepcopy() (in module mvpa2.misc.support) descr (mvpa2.misc.transformers.ClassWithCollections attribute) destroy() (mvpa2.misc.cmdline.OptionGroup method) (mvpa2.misc.cmdline.OptionParser method) detrending development development snapshot

disable_interspersed_args() (mvpa2.misc.cmdline.OptionParser method) dissimilarity matrix distance (mvpa2.atlases.ReferencesAtlas attribute) distance_func (mvpa2.misc.neighborhood.Sphere attribute) DistPValue (class in mvpa2.misc.transformers) Documentation overview double_gamma_hrf() (in module mvpa2.misc.fx) Download DSMatrix (class in mvpa2.misc.stats) dual_gaussian() (in module mvpa2.misc.fx) dumb_feature_binary_dataset() (in module mvpa2.misc.data_generators) dumb_feature_dataset() (in module mvpa2.misc.data_generators)

E

element_sizes (mvpa2.misc.neighborhood.Sphere attribute) enable_interspersed_args() (mvpa2.misc.cmdline.OptionParser method) enabled (mvpa2.misc.transformers.ConditionalAttribute attribute) environment variable MVPA_DEBUG, [1], [2] MVPA_DEBUG_METRICS MVPA_DEBUG_WTF MVPA_EXAMPLES_INTERACTIVE MVPA_MATPLOTLIB_BACKEND MVPA_QUICKTEST MVPA_SEED MVPA_SVM_BACKEND MVPA_TESTS_LABILE, [1] MVPA_TESTS_QUICK, [1] MVPA_VERBOSE MVPA_VERBOSE_OUTPUT MVPA_WARNINGS_BT MVPA_WARNINGS_COUNT, [1] MVPA_WARNINGS_SUPPRESS Epoch error() (mvpa2.misc.cmdline.OptionParser method) Event (class in mvpa2.misc.support)

event-related fMRI, [1] example examples Exemplar exit() (mvpa2.misc.cmdline.OptionParser method) expand_prog_name() (mvpa2.misc.cmdline.OptionParser method)

F

Feature Feature attribute Feature Selection feature selection feature_ids Fedora find() (mvpa2.atlases.FSLProbabilisticAtlas method) find_collection() (mvpa2.misc.data_generators.Dataset method) first_axis_mean() (in module mvpa2.misc.transformers) first_axis_sum_not_zero() (in module mvpa2.misc.transformers)

fit2histogram() (in module mvpa2.misc.fx) fMRI format_epilog() (mvpa2.misc.cmdline.OptionParser method) format_help() (mvpa2.misc.cmdline.OptionGroup method) (mvpa2.misc.cmdline.OptionParser method) format_option_help() (mvpa2.misc.cmdline.OptionParser method) free software from_channeltimeseries() (mvpa2.misc.data_generators.Dataset class method) from_wizard() (mvpa2.misc.data_generators.Dataset class method) FSL, [1] FSLProbabilisticAtlas (class in mvpa2.atlases)

G

Generalization get_attr() (mvpa2.misc.data_generators.Dataset method) get_break_points() (in module mvpa2.misc.support) get_default_values() (mvpa2.misc.cmdline.OptionParser method) get_description() (mvpa2.misc.cmdline.OptionParser method) get_full_matrix() (mvpa2.misc.stats.DSMatrix method) get_limit_filter() (in module mvpa2.misc.support) get_map() (mvpa2.atlases.FSLProbabilisticAtlas method) get_mapped() (mvpa2.misc.data_generators.Dataset method) get_maps() (mvpa2.atlases.FSLProbabilisticAtlas method) get_metric() (mvpa2.misc.stats.DSMatrix method) get_mv_pattern() (in module mvpa2.misc.data_generators) get_nelements_per_value() (in module mvpa2.misc.support)

get_opt_string() (mvpa2.misc.cmdline.Option method) get_option_group() (mvpa2.misc.cmdline.OptionParser method) get_prog_name() (mvpa2.misc.cmdline.OptionParser method) get_triangle() (mvpa2.misc.stats.DSMatrix method) get_usage() (mvpa2.misc.cmdline.OptionParser method) get_vector_form() (mvpa2.misc.stats.DSMatrix method) get_version() (mvpa2.misc.cmdline.OptionParser method) Git, [1] Git repository GPR, [1] grand_mean() (in module mvpa2.misc.transformers) group_kwargs() (in module mvpa2.misc.args)

H

history hlcuster

HollowSphere (class in mvpa2.misc.neighborhood) hyperalignment, [1]

I

Identity() (in module mvpa2.misc.transformers) idhash (mvpa2.misc.data_generators.Dataset attribute) idhash() (in module mvpa2.misc.support) idhash_() (in module mvpa2.misc.neighborhood) indent_doc() (in module mvpa2.misc.support) IndexQueryEngine (class in mvpa2.misc.neighborhood) inner_radius (mvpa2.misc.neighborhood.HollowSphere attribute) installation

introduction invariant features IPython is_in_volume() (in module mvpa2.misc.support) is_sorted() (in module mvpa2.misc.support) isSequenceType() (in module mvpa2.misc.attrmap) (in module mvpa2.misc.support) item() (mvpa2.misc.data_generators.Dataset method) iteritems() (mvpa2.misc.attrmap.AttributeMap method)

K

keys() (mvpa2.misc.attrmap.AttributeMap method)

kNN

L

l1_normed() (in module mvpa2.misc.transformers) l2_normed() (in module mvpa2.misc.transformers) Label label_voxel() (mvpa2.atlases.FSLProbabilisticAtlas method) (mvpa2.atlases.LabelsAtlas method) (mvpa2.atlases.ReferencesAtlas method) LabelsAtlas (class in mvpa2.atlases) Learner least_sq_fit() (in module mvpa2.misc.fx) levels_listing() (mvpa2.atlases.ReferencesAtlas method)

LIBSVM, [1] license linear1d_gaussian_noise() (in module mvpa2.misc.data_generators) linear_awgn() (in module mvpa2.misc.data_generators) ListType (in module mvpa2.misc.support) load_datadb_demo_blockfmri() (in module mvpa2.misc.data_generators) load_datadb_tutorial_data() (in module mvpa2.misc.data_generators) load_example_fmri_dataset() (in module mvpa2.misc.data_generators)

M

Machine Learning MacOS X, [1], [2] MapOverlap (class in mvpa2.misc.support) MappedClassifier mapper, [1] (mvpa2.misc.data_generators.Dataset attribute) mask2slice() (in module mvpa2.misc.support) match_accuracy() (in module mvpa2.misc.errorfx) Matlab matplotlib max_of_abs() (in module mvpa2.misc.transformers) MDP mean_match_accuracy() (in module mvpa2.misc.errorfx) mean_mismatch_error() (in module mvpa2.misc.errorfx) mean_power_fx() (in module mvpa2.misc.errorfx) Meta-classifier misc mismatch_error() (in module mvpa2.misc.errorfx) model selection, [1] modular architecture monte-carlo, [1] motion correction multiple_chunks() (in module mvpa2.misc.data_generators) MVPA, [1] MVPA toolbox for Matlab, [1] mvpa2.atlases (module) mvpa2.misc (module) mvpa2.misc.args (module)

mvpa2.misc.attrmap (module) mvpa2.misc.cmdline (module) mvpa2.misc.data_generators (module) mvpa2.misc.errorfx (module) mvpa2.misc.exceptions (module) mvpa2.misc.fx (module) mvpa2.misc.neighborhood (module) mvpa2.misc.sampleslookup (module) mvpa2.misc.stats (module) mvpa2.misc.support (module) mvpa2.misc.transformers (module) mvpa2.misc.vproperty (module) MVPA_DEBUG, [1], [2] MVPA_DEBUG_METRICS MVPA_DEBUG_WTF MVPA_EXAMPLES_INTERACTIVE MVPA_MATPLOTLIB_BACKEND MVPA_QUICKTEST MVPA_SEED MVPA_SVM_BACKEND MVPA_TESTS_LABILE, [1] MVPA_TESTS_QUICK, [1] MVPA_VERBOSE MVPA_VERBOSE_OUTPUT MVPA_WARNINGS_BT MVPA_WARNINGS_COUNT, [1] MVPA_WARNINGS_SUPPRESS

N

Neural Data Modality NiBabel NIfTI

noisy_2d_fx() (in module mvpa2.misc.data_generators) normal_feature_dataset() (in module mvpa2.misc.data_generators) NumPy

O

O (mvpa2.misc.data_generators.Dataset attribute) one_minus() (in module mvpa2.misc.transformers) OpenSUSE, [1] optimization Option (class in mvpa2.misc.cmdline)

OptionGroup (class in mvpa2.misc.cmdline) OptionGroups (class in mvpa2.misc.cmdline) OptionParser (class in mvpa2.misc.cmdline) Options (class in mvpa2.misc.cmdline) OverAxis (class in mvpa2.misc.transformers)

P

parse() (mvpa2.misc.support.SmartVersion method) parse_args() (mvpa2.misc.cmdline.OptionParser method) pearsonr() (in module mvpa2.misc.errorfx) permutation, [1] plotting plotting example print_help() (mvpa2.misc.cmdline.OptionParser method) print_usage() (mvpa2.misc.cmdline.OptionParser method)

print_version() (mvpa2.misc.cmdline.OptionParser method) process() (mvpa2.misc.cmdline.Option method) Processing object progress tracking Publications pure_multivariate_signal() (in module mvpa2.misc.data_generators) PyMatlab PyMVPA poster

Q

query() (mvpa2.misc.neighborhood.CachedQueryEngine method) (mvpa2.misc.neighborhood.IndexQueryEngine method) (mvpa2.misc.neighborhood.QueryEngineInterface method) query_byid() (mvpa2.misc.neighborhood.CachedQueryEngine method) (mvpa2.misc.neighborhood.QueryEngine method) (mvpa2.misc.neighborhood.QueryEngineInterface method) QueryEngine (class in mvpa2.misc.neighborhood)

queryengine (mvpa2.misc.neighborhood.CachedQueryEngine attribute) QueryEngineInterface (class in mvpa2.misc.neighborhood)

R

R radius (mvpa2.misc.neighborhood.Sphere attribute) random number generation rank_order() (in module mvpa2.misc.transformers) recommended software redirecting output reference_level (mvpa2.atlases.ReferencesAtlas attribute) references ReferencesAtlas (class in mvpa2.atlases) relative_rms_error() (in module mvpa2.misc.errorfx) release notes, [1]

releases required software reset() (mvpa2.misc.transformers.ClassWithCollections method) (mvpa2.misc.transformers.ConditionalAttribute method) reuse_absolute_path() (in module mvpa2.misc.support) reverse_rank_order() (in module mvpa2.misc.transformers) review rfe_history_to_maps() (in module mvpa2.misc.support) rms_error() (in module mvpa2.misc.errorfx) RNG root_mean_power_fx() (in module mvpa2.misc.errorfx) RPy, [1]

S

S (mvpa2.misc.data_generators.Dataset attribute) Sample Sample attribute SamplesLookup (class in mvpa2.misc.sampleslookup) SciPy searchlight, [1] Searchlight second_axis_mean() (in module mvpa2.misc.transformers) self-organizing map Sensitivity sensitivity, [1] Sensitivity Map set_attr() (mvpa2.misc.data_generators.Dataset method) set_default() (mvpa2.misc.cmdline.OptionParser method) set_defaults() (mvpa2.misc.cmdline.OptionParser method) set_distance() (mvpa2.atlases.ReferencesAtlas method) set_process_default_values() (mvpa2.misc.cmdline.OptionParser method) set_reference_level() (mvpa2.atlases.ReferencesAtlas method) set_title() (mvpa2.misc.cmdline.OptionGroup method) set_usage() (mvpa2.misc.cmdline.OptionParser method) settings Shogun SimpleSOMMapper

sin_modulated() (in module mvpa2.misc.data_generators) single_gamma_hrf() (in module mvpa2.misc.fx) SmartVersion (class in mvpa2.misc.support) SMLR SOM sorted (mvpa2.misc.neighborhood.IndexQueryEngine attribute) source package Spatial Discrimination Map (SDM) Sphere (class in mvpa2.misc.neighborhood) split_kwargs() (in module mvpa2.misc.args) standard_option_list (mvpa2.misc.cmdline.OptionParser attribute) Statistical Discrimination Map (SDM) Statistical Learning statistical testing STORE_ACTIONS (mvpa2.misc.cmdline.Option attribute) StringType (in module mvpa2.misc.support) suggested software sum_of_abs() (in module mvpa2.misc.transformers) Supervised Support SVD SVM SWIG

T

T (mvpa2.misc.data_generators.Dataset attribute) take_action() (mvpa2.misc.cmdline.Option method) takes_value() (mvpa2.misc.cmdline.Option method) Target targets (mvpa2.misc.data_generators.Dataset attribute) Testing Dataset textbook Time-compression to_literal() (mvpa2.misc.attrmap.AttributeMap method) to_numeric() (mvpa2.misc.attrmap.AttributeMap method)

todo train() (mvpa2.misc.neighborhood.CachedQueryEngine method) (mvpa2.misc.neighborhood.QueryEngine method) (mvpa2.misc.neighborhood.QueryEngineInterface method) (mvpa2.misc.neighborhood.Sphere method) Training Dataset transform_with_boxcar() (in module mvpa2.misc.support) trapz() (in module mvpa2.misc.errorfx) TupleType (in module mvpa2.misc.support) Tutorial, [1], [2], [3], [4], [5], [6], [7], [8], [9] TYPE_CHECKER (mvpa2.misc.cmdline.Option attribute) TYPED_ACTIONS (mvpa2.misc.cmdline.Option attribute) TYPES (mvpa2.misc.cmdline.Option attribute)

U

Ubuntu UC (mvpa2.misc.data_generators.Dataset attribute) unique_combinations() (in module mvpa2.misc.support) uniquechunks (mvpa2.misc.data_generators.Dataset attribute)

uniquetargets (mvpa2.misc.data_generators.Dataset attribute) unittests untrain() (mvpa2.misc.neighborhood.CachedQueryEngine method) UT (mvpa2.misc.data_generators.Dataset attribute)

V

value2idx() (in module mvpa2.misc.support) values() (mvpa2.misc.attrmap.AttributeMap method) variance_1sv() (in module mvpa2.misc.errorfx) verbosity, [1]

Version (class in mvpa2.misc.support) version_to_tuple() (in module mvpa2.misc.support) VProperty (class in mvpa2.misc.vproperty)

W

warning, [1] Weight Vector Who is using it?

Windows Windows installer wr1996() (in module mvpa2.misc.data_generators)

X

xunique_combinations() (in module mvpa2.misc.support)