_images/cosmomvpa_banner.png

A multi-modal, multi-variate pattern analysis (MVPA) toolbox in Matlab / GNU Octave for cognitive neuroscientists.

CoSMoMVPA

  • State-of-the art, yet simple to use MVPA implementations.
  • Runs on the Matlab and GNU Octave platform, on MS Windows, OSX, and GNU/Linux.
  • Handles fMRI volumetric, fMRI surface-based, and MEEG data through a uniform data structure.
  • Support for a wide range of data formats.
  • Searchlights in the volume, on the surface, over sensors, time bins, and frequency bands.
  • Multiple-comparison correction using Threshold-Free Cluster Enhancement Monte Carlo simulations.
  • Extensive documentation, including a variety of runnable scripts and implementation exercises (with solutions).
  • Is Free/Open Source Software (MIT License), see http://github.com/CoSMoMVPA/CoSMoMVPA.
_images/icon_demos.png _images/icon_philosophy.png _images/icon_get_started.png _images/icon_download.png _images/icon_modules.png _images/icon_documentation.png _images/icon_exercises.png _images/icon_tips.png _images/icon_faq.png _images/icon_contact.png _images/icon_develop.png _images/icon_thanks.png

News

  • our CoSMoMVPA manuscript has been published ([OCH16]): Oosterhof, N. N., Connolly, A. C., and Haxby, J. V. (2016). CoSMoMVPA: multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave. Frontiers in Neuroinformatics, doi:10.3389/fninf.2016.00027.

Changes since last month

Summary

 [BF]    3 bug fixes
[BIG]    2 major changes
[BLD]    4 changes in build system
[CLN]    1 clean-ups
[DOC]    1 code documentation changes
[ENH]    7 enhancements
 [NF]    6 new features
 [RF]    4 refactorings
[SML]    1 minor changes
[TST]   14 unit or doctest changes
[WEB]    5 website documentation changes

Acknowledgements

- Luca Ronconi
- Luca Turella

Major changes

commit a69f1ab0c5247f085418323973a5160e2c77f4d0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jan 19 20:33:04 2017 +0100

    TST+BIG: change test functions to be able to run test at recent
        (2016 and later) versions of Matlab

 tests/test_align.m                                | 5 ++++-
 tests/test_anova_feature_selector.m               | 4 ++++
 tests/test_average_samples.m                      | 5 ++++-
 tests/test_balance_partitions.m                   | 5 ++++-
 tests/test_cartprod.m                             | 5 ++++-
 tests/test_check_dataset.m                        | 5 ++++-
 tests/test_check_external.m                       | 5 ++++-
 tests/test_check_neighborhood.m                   | 5 ++++-
 tests/test_check_partitions.m                     | 5 ++++-
 tests/test_chunkize.m                             | 5 ++++-
 tests/test_classify.m                             | 5 ++++-
 tests/test_cluster_neighborhood.m                 | 5 ++++-
 tests/test_clusterize.m                           | 5 ++++-
 tests/test_config.m                               | 5 ++++-
 tests/test_confusion_matrix.m                     | 5 ++++-
 tests/test_convert_neighborhood.m                 | 5 ++++-
 tests/test_corr.m                                 | 5 ++++-
 tests/test_correlation_measure.m                  | 5 ++++-
 tests/test_cosmo_dataset_operations.m             | 4 ++++
 tests/test_cosmo_fmri_dataset.m                   | 5 ++++-
 tests/test_cross_neighborhood.m                   | 5 ++++-
 tests/test_crossvalidate.m                        | 5 ++++-
 tests/test_crossvalidation_measure.m              | 5 ++++-
 tests/test_dim_find.m                             | 5 ++++-
 tests/test_dim_generalization_measure.m           | 5 ++++-
 tests/test_dim_insert.m                           | 5 ++++-
 tests/test_dim_match.m                            | 5 ++++-
 tests/test_dim_prune.m                            | 5 ++++-
 tests/test_dim_remove.m                           | 5 ++++-
 tests/test_dim_rename.m                           | 5 ++++-
 tests/test_dim_slice.m                            | 5 ++++-
 tests/test_dim_transpose.m                        | 5 ++++-
 tests/test_dir.m                                  | 5 ++++-
 tests/test_disp.m                                 | 5 ++++-
 tests/test_dissimilarity_matrix_measure.m         | 5 ++++-
 tests/test_distatis.m                             | 5 ++++-
 tests/test_external_neuroelf.m                    | 5 ++++-
 tests/test_external_surfing.m                     | 5 ++++-
 tests/test_find_local_extrema.m                   | 5 ++++-
 tests/test_flatten.m                              | 5 ++++-
 tests/test_fmri_convert_xform.m                   | 5 ++++-
 tests/test_fmri_dataset.m                         | 5 ++++-
 tests/test_fmri_deoblique.m                       | 5 ++++-
 tests/test_fmri_io.m                              | 4 ++++
 tests/test_fmri_orientation.m                     | 5 ++++-
 tests/test_fx.m                                   | 5 ++++-
 tests/test_independent_samples_partitioner.m      | 5 ++++-
 tests/test_index_unique.m                         | 5 ++++-
 tests/test_interval_neighborhood.m                | 5 ++++-
 tests/test_isequaln.m                             | 4 ++++
 tests/test_isfield.m                              | 5 ++++-
 tests/test_map_pca.m                              | 5 ++++-
 tests/test_mask_dim_intersect.m                   | 5 ++++-
 tests/test_match.m                                | 5 ++++-
 tests/test_measure_clusters.m                     | 5 ++++-
 tests/test_meeg_baseline_correct.m                | 5 ++++-
 tests/test_meeg_chan_neighborhood.m               | 5 ++++-
 tests/test_meeg_chan_neighbors.m                  | 5 ++++-
 tests/test_meeg_chantype.m                        | 5 ++++-
 tests/test_meeg_find_layout.m                     | 5 ++++-
 tests/test_meeg_io.m                              | 5 ++++-
 tests/test_meeg_layout_collection.m               | 5 ++++-
 tests/test_meeg_read_layout.m                     | 5 ++++-
 tests/test_meeg_senstype_collection.m             | 5 ++++-
 tests/test_meeg_source.m                          | 5 ++++-
 tests/test_montecarlo_cluster_stat.m              | 5 ++++-
 tests/test_montecarlo_cluster_stat_distribution.m | 5 ++++-
 tests/test_naive_bayes_classifier_searchlight.m   | 5 ++++-
 tests/test_neighborhood_split.m                   | 5 ++++-
 tests/test_normalize.m                            | 5 ++++-
 tests/test_oddeven_partitioner.m                  | 5 ++++-
 tests/test_parallel_get_nproc_available.m         | 5 ++++-
 tests/test_parcellfun.m                           | 5 ++++-
 tests/test_partitions.m                           | 5 ++++-
 tests/test_pca.m                                  | 5 ++++-
 tests/test_pdist.m                                | 5 ++++-
 tests/test_plot_slices.m                          | 5 ++++-
 tests/test_publish_run_scripts.m                  | 5 ++++-
 tests/test_rand.m                                 | 5 ++++-
 tests/test_randomize_targets.m                    | 5 ++++-
 tests/test_randperm.m                             | 5 ++++-
 tests/test_remove_useless_data.m                  | 5 ++++-
 tests/test_run_tests.m                            | 5 ++++-
 tests/test_sample_unique.m                        | 5 ++++-
 tests/test_searchlight.m                          | 5 ++++-
 tests/test_show_progress.m                        | 5 ++++-
 tests/test_slice.m                                | 5 ++++-
 tests/test_spherical_neighborhood.m               | 5 ++++-
 tests/test_split.m                                | 5 ++++-
 tests/test_squareform.m                           | 5 ++++-
 tests/test_stack.m                                | 5 ++++-
 tests/test_stat.m                                 | 5 ++++-
 tests/test_statcode.m                             | 5 ++++-
 tests/test_strjoin.m                              | 5 ++++-
 tests/test_strsplit.m                             | 5 ++++-
 tests/test_structjoin.m                           | 5 ++++-
 tests/test_surface_io.m                           | 5 ++++-
 tests/test_surficial_io_gifti.m                   | 5 ++++-
 tests/test_surficial_io_niml_dset.m               | 5 ++++-
 tests/test_surficial_neighborhood.m               | 5 ++++-
 tests/test_synthetic_dataset.m                    | 5 ++++-
 tests/test_tail.m                                 | 5 ++++-
 tests/test_target_dsm_corr_measure.m              | 5 ++++-
 tests/test_type.m                                 | 5 ++++-
 tests/test_vol_coordinates.m                      | 5 ++++-
 tests/test_vol_grid_convert.m                     | 5 ++++-
 tests/test_warning.m                              | 5 ++++-
 tests/test_wtf.m                                  | 5 ++++-
 108 files changed, 432 insertions(+), 104 deletions(-)

Bug fixes

commit 1e52b2ba11fdc780a3836d8774a234258caf0237
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Feb 9 11:27:31 2017 +0100

    BF+TST+ACK: fix returning the number of processes available to be
        never more than the number of processes requested. Thanks to
        #Luca Turella# for the fix

 mvpa/cosmo_parallel_get_nproc_available.m | 53 +++++++++++++++++++++++++------
 tests/test_parallel_get_nproc_available.m | 38 ++++++++++++++++++++--
 2 files changed, 79 insertions(+), 12 deletions(-)

commit 6aef57d758dea29fb3fb94aacc2ef73ce729c5b0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Feb 9 11:09:06 2017 +0100

    BF+ACK: deal properly with cases when niter <= nproc_available.
        Thanks to #Luca Turella# for the report

 mvpa/cosmo_montecarlo_cluster_stat.m | 24 +++++++++++++++++-------
 tests/test_montecarlo_cluster_stat.m | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 7 deletions(-)

commit 6a54d02dea58557ce331748bb89e8d380b135c18
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Feb 8 19:35:21 2017 +0100

    BF+ACK: use proper variable name. Thanks to #Luca Turella# for the
        report

 mvpa/cosmo_parallel_get_nproc_available.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

All changes

commit dd59db99b1b04f6fa49fc65ba0d5ccf846c6e85c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Feb 14 11:46:43 2017 +0100

    WEB: explain use of onCleanup

 doc/source/contribute.rst | 40 ++++++++++++++++++++++++++++++++++++++--
 1 file changed, 38 insertions(+), 2 deletions(-)

commit 44e51f5b6be3fc22b56f991e882412bd2b9b8786
Merge: 415ec90 a5f2af9
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Feb 13 18:48:54 2017 +0100

    Merge branch 'octave/struct_parallel_package'

commit a5f2af956cbcee42a3453efd3d5e7df529d4fc60
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Feb 13 18:48:33 2017 +0100

    MSC: year is 2017

 COPYING | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

commit 415ec90ee456be68da4a03ffac05f9f2b7b7512d
Merge: c287da2 397acf2
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sat Feb 11 21:58:03 2017 +0100

    Merge pull request #133 from nno/octave/struct_parallel_package
        BLD: load parallel and struct package, and install recent GCC

commit 397acf20c0e50bcbab064a1c1e039f0ffa6c8a43
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Feb 11 20:37:45 2017 +0100

    BLD: back to GCC 4.8

 .travis.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit fbc4a3a2328f76b4c60709a86f2a368128a9efba
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Feb 11 17:35:33 2017 +0100

    BLD: try GCC 4.6

 .travis.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit 132af46f8e52c3e1366650ac77daa1c51f8d1185
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Feb 11 17:23:36 2017 +0100

    BLD: load parallel and struct package, and install recent GCC

 .travis.yml | 69 +++++++++++++++++++++++++++++++++++++++++++++++--------------
 1 file changed, 54 insertions(+), 15 deletions(-)

commit c287da2e22b5419dc62d4be7e29c5baa7ea5227d
Merge: dc7f6c7 c71d8e7
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Feb 10 16:50:58 2017 +0100

    Merge pull request #132 from nno/_enh/parallel_quick_nproc_eq_1
        ENH+RF: do not show warning if nproc=inf

commit dc7f6c7420ee9d56e73daeb690a6521748f14a20
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 15:45:56 2017 +0100

    WEB: introduce new FT tag for git

 doc/source/contribute.rst | 8 ++++----
 doc/source/links.txt      | 4 +++-
 2 files changed, 7 insertions(+), 5 deletions(-)

commit 13f003eb5e683f35a0e85d24393936a0980d5aa7
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 15:45:14 2017 +0100

    WEB: add some testing guidelines

 doc/source/contribute.rst | 41 +++++++++++++++++++++++++++++++++--------
 1 file changed, 33 insertions(+), 8 deletions(-)

commit f32d07aa286e1c44c99b2c66ebf5a633800d9ea2
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 15:44:51 2017 +0100

    WEB: add explanations about coding guidelines

 doc/source/contribute.rst | 52 +++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 43 insertions(+), 9 deletions(-)

commit 37bf229361beacf0775a8cc03e4e5e110d667705
Merge: 594a0b6 9a76530
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 15:43:47 2017 +0100

    Merge branch 'master' of https://github.com/CoSMoMVPA/CoSMoMVPA

commit 9a765305e171e8c6cdcf4a153782e6aaa4f55c88
Merge: 22cb6b0 c1d4f04
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Feb 10 15:42:58 2017 +0100

    Merge pull request #130 from nno/_nf/eeglab_io_itc_ersp
        NF: support for EEGLAB ITC and ERSP data

commit c1d4f04793f0d864094279ac2bcd94db10ef98c4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 14:26:37 2017 +0100

    TF: properly select ersp or erspbase data

 mvpa/cosmo_meeg_dataset.m | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

commit 2b1227b92a2cd106ca919c3314bd3fc40898f990
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 13:37:01 2017 +0100

    DOC: update documentation refleccting what ERSP data in EEGLAB
        might represent

 mvpa/cosmo_map2meeg.m     |  5 ++++-
 mvpa/cosmo_meeg_dataset.m | 41 +++++++++++++++++++++++++++++------------
 2 files changed, 33 insertions(+), 13 deletions(-)

commit c71d8e7f6b984267ae005d56fae249df5756467b
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Feb 10 11:36:50 2017 +0100

    ENH+RF: do not show warning  if nproc=inf; do not require starting
        parallel pool if nproc=1

 mvpa/cosmo_parallel_get_nproc_available.m | 38 +++++++++++++++++++++++++------
 tests/test_parallel_get_nproc_available.m |  4 ++--
 2 files changed, 33 insertions(+), 9 deletions(-)

commit 594a0b6660f841920b1c16d2cdd62355c37c2fa9
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Feb 9 17:43:51 2017 +0100

    TST: smaller dataset for testing

 tests/test_cross_neighborhood.m | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

commit 22cb6b04ba40a3c41c7767ebf9be2b9383ca71a5
Merge: 0286c96 1e52b2b
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Thu Feb 9 12:59:47 2017 +0100

    Merge pull request #131 from nno/_nf/matlabpool          NF:
        support for matlabpool

commit 1e52b2ba11fdc780a3836d8774a234258caf0237
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Feb 9 11:27:31 2017 +0100

    BF+TST+ACK: fix returning the number of processes available to be
        never more than the number of processes requested. Thanks to
        #Luca Turella# for the fix

 mvpa/cosmo_parallel_get_nproc_available.m | 53 +++++++++++++++++++++++++------
 tests/test_parallel_get_nproc_available.m | 38 ++++++++++++++++++++--
 2 files changed, 79 insertions(+), 12 deletions(-)

commit 6aef57d758dea29fb3fb94aacc2ef73ce729c5b0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Feb 9 11:09:06 2017 +0100

    BF+ACK: deal properly with cases when niter <= nproc_available.
        Thanks to #Luca Turella# for the report

 mvpa/cosmo_montecarlo_cluster_stat.m | 24 +++++++++++++++++-------
 tests/test_montecarlo_cluster_stat.m | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 7 deletions(-)

commit 6a54d02dea58557ce331748bb89e8d380b135c18
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Feb 8 19:35:21 2017 +0100

    BF+ACK: use proper variable name. Thanks to #Luca Turella# for the
        report

 mvpa/cosmo_parallel_get_nproc_available.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit e45d0fa0e797cb1e18b36bb42a51b4ef8d9c43f6
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Feb 8 18:38:37 2017 +0100

    NF+TST: support for parallel toolbox for Matlab < 2013b, which
        uses matlabpool instead of parpool

 mvpa/cosmo_parallel_get_nproc_available.m | 43 ++++++++++++++++++++++++++--
 mvpa/cosmo_parcellfun.m                   |  1 +
 tests/test_parallel_get_nproc_available.m | 47 +++++++++++++++++++++++++++++--
 3 files changed, 86 insertions(+), 5 deletions(-)

commit 69b5be2eabb5e1d66e279a92b2df79610ca8ebc4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Feb 8 18:12:47 2017 +0100

    NF: support for cosmo_wtf('versin_number')

 mvpa/cosmo_wtf.m |  9 +++++++++
 tests/test_wtf.m | 11 +++++++++++
 2 files changed, 20 insertions(+)

commit 0286c96113b6d7bd79343499d2afe2ad54181bcc
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Feb 8 14:22:38 2017 +0100

    FAQ+WEB+ACK: describe how to compute average for subset of
        channels. Answers question by Evelyn Muschter#

 doc/source/faq.rst | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

commit ba16f08f3b5c0744e573b485c4873e5e73ce018e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Feb 7 18:49:22 2017 +0100

    NF+TST: support for reading EEGLAB ERSP data

 mvpa/cosmo_map2meeg.m     |  11 ++--
 mvpa/cosmo_meeg_dataset.m | 118 ++++++++++++++++++++++++++++++++--------
 tests/test_meeg_io.m      | 133 +++++++++++++++++++++++++++++++++++++---------
 3 files changed, 211 insertions(+), 51 deletions(-)

commit c65bb972d0730d140ffe4b6c313495fc87a7a52e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Feb 7 16:57:26 2017 +0100

    NF+TST+ACK: support for EEGLAB ITC data. Feature requested by
        #Luca Ronconi#

 mvpa/cosmo_map2meeg.m     | 29 ++++++++++++++++++++++-------
 mvpa/cosmo_meeg_dataset.m |  7 +++++--
 tests/test_meeg_io.m      |  4 ++--
 3 files changed, 29 insertions(+), 11 deletions(-)

commit 6fa24949ce1c385823a4e063b28ee1bc9ae35c0c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Feb 7 16:24:22 2017 +0100

    TST+RF: refactor test for EEGLAB I/O

 tests/test_meeg_io.m | 95 +++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 79 insertions(+), 16 deletions(-)

commit 0b5176360bd0be8abbede61e8459312ce65572d9
Merge: a19a8ce 507671a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Jan 20 18:26:42 2017 +0100

    Merge pull request #129 from nno/_compat/matlab2016_localfunctions
        TST+BIG: change test functions to be able to run test at
        recent versions of Matlab

commit 507671ab4c08997a551f70bc44971969b9f7583e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 17:00:34 2017 +0100

    ENH: use cosmo_warning instead of warning

 mvpa/cosmo_parallel_get_nproc_available.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 37e3dad3b545b6c77837867e1afa613794f44005
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 16:45:02 2017 +0100

    CMPT: use scalar values with error for compatibility with early
        versions of Matlab

 mvpa/cosmo_vol_coordinates.m | 2 +-
 tests/test_crossvalidate.m   | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

commit 00763dd57315eebc8792dbbd349e17e287eba516
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 16:03:39 2017 +0100

    TST: do not show warning when testing for exceptions

 tests/test_parallel_get_nproc_available.m | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

commit 48df59b68512980337d02080c7f1b5ce28f287d5
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 15:57:02 2017 +0100

    CLN: remove unused lines

 mvpa/cosmo_parallel_get_nproc_available.m | 3 ---
 1 file changed, 3 deletions(-)

commit ff9f1222af0a25f54bbb5a0450af5bf85cb3494d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 15:31:32 2017 +0100

    RF: ensure that number of available processors is always set

 mvpa/cosmo_parallel_get_nproc_available.m | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

commit a05a48ef0025a916e9fc87c5e04b6d1f5eea74c4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 15:14:30 2017 +0100

    ENH+TST: ensure that no warning is given when the number of cores
        is not specified

 mvpa/cosmo_parallel_get_nproc_available.m | 135 +++++++++++++-----------------
 tests/test_parcellfun.m                   |  18 ++++
 2 files changed, 76 insertions(+), 77 deletions(-)

commit b407f8d8b453594442935fb2fe24b80cb14d5e62
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 15:12:05 2017 +0100

    CMPT+TST: avoid warning message of obsolete svmtrain in recent
        versions of Matlab

 mvpa/cosmo_classify_matlabsvm_2class.m | 46 +++++++++++++++++++++++++++++-----
 tests/test_classify.m                  | 31 ++++++++++++-----------
 2 files changed, 56 insertions(+), 21 deletions(-)

commit 1c65e09dee0fe0967f439fe29a8de316f39099d3
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 11:10:30 2017 +0100

    TST+CMPT: change selection of directory output to accomodate
        change in output (empty versus struct of size 0x1) in recent
        versions of Matlab

 mvpa/cosmo_dir.m | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

commit 1f058c26334178a63b2fc88c0d7fbdc9182d1bdf
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 11:05:06 2017 +0100

    ENH: use uniform approach for single and multi thread computation,
        resulting in uniform error message in case of no uniform
        output

 mvpa/cosmo_parcellfun.m | 6 +++---
 tests/test_parcellfun.m | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

commit 0415458fb3c097f94e798b302559cb2bfad68612
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jan 20 10:41:56 2017 +0100

    CMPT+TST: update test to include localfunctions, for Matlab >=
        2016

 tests/test_run_tests.m | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

commit a69f1ab0c5247f085418323973a5160e2c77f4d0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jan 19 20:33:04 2017 +0100

    TST+BIG: change test functions to be able to run test at recent
        (2016 and later) versions of Matlab

 tests/test_align.m                                | 5 ++++-
 tests/test_anova_feature_selector.m               | 4 ++++
 tests/test_average_samples.m                      | 5 ++++-
 tests/test_balance_partitions.m                   | 5 ++++-
 tests/test_cartprod.m                             | 5 ++++-
 tests/test_check_dataset.m                        | 5 ++++-
 tests/test_check_external.m                       | 5 ++++-
 tests/test_check_neighborhood.m                   | 5 ++++-
 tests/test_check_partitions.m                     | 5 ++++-
 tests/test_chunkize.m                             | 5 ++++-
 tests/test_classify.m                             | 5 ++++-
 tests/test_cluster_neighborhood.m                 | 5 ++++-
 tests/test_clusterize.m                           | 5 ++++-
 tests/test_config.m                               | 5 ++++-
 tests/test_confusion_matrix.m                     | 5 ++++-
 tests/test_convert_neighborhood.m                 | 5 ++++-
 tests/test_corr.m                                 | 5 ++++-
 tests/test_correlation_measure.m                  | 5 ++++-
 tests/test_cosmo_dataset_operations.m             | 4 ++++
 tests/test_cosmo_fmri_dataset.m                   | 5 ++++-
 tests/test_cross_neighborhood.m                   | 5 ++++-
 tests/test_crossvalidate.m                        | 5 ++++-
 tests/test_crossvalidation_measure.m              | 5 ++++-
 tests/test_dim_find.m                             | 5 ++++-
 tests/test_dim_generalization_measure.m           | 5 ++++-
 tests/test_dim_insert.m                           | 5 ++++-
 tests/test_dim_match.m                            | 5 ++++-
 tests/test_dim_prune.m                            | 5 ++++-
 tests/test_dim_remove.m                           | 5 ++++-
 tests/test_dim_rename.m                           | 5 ++++-
 tests/test_dim_slice.m                            | 5 ++++-
 tests/test_dim_transpose.m                        | 5 ++++-
 tests/test_dir.m                                  | 5 ++++-
 tests/test_disp.m                                 | 5 ++++-
 tests/test_dissimilarity_matrix_measure.m         | 5 ++++-
 tests/test_distatis.m                             | 5 ++++-
 tests/test_external_neuroelf.m                    | 5 ++++-
 tests/test_external_surfing.m                     | 5 ++++-
 tests/test_find_local_extrema.m                   | 5 ++++-
 tests/test_flatten.m                              | 5 ++++-
 tests/test_fmri_convert_xform.m                   | 5 ++++-
 tests/test_fmri_dataset.m                         | 5 ++++-
 tests/test_fmri_deoblique.m                       | 5 ++++-
 tests/test_fmri_io.m                              | 4 ++++
 tests/test_fmri_orientation.m                     | 5 ++++-
 tests/test_fx.m                                   | 5 ++++-
 tests/test_independent_samples_partitioner.m      | 5 ++++-
 tests/test_index_unique.m                         | 5 ++++-
 tests/test_interval_neighborhood.m                | 5 ++++-
 tests/test_isequaln.m                             | 4 ++++
 tests/test_isfield.m                              | 5 ++++-
 tests/test_map_pca.m                              | 5 ++++-
 tests/test_mask_dim_intersect.m                   | 5 ++++-
 tests/test_match.m                                | 5 ++++-
 tests/test_measure_clusters.m                     | 5 ++++-
 tests/test_meeg_baseline_correct.m                | 5 ++++-
 tests/test_meeg_chan_neighborhood.m               | 5 ++++-
 tests/test_meeg_chan_neighbors.m                  | 5 ++++-
 tests/test_meeg_chantype.m                        | 5 ++++-
 tests/test_meeg_find_layout.m                     | 5 ++++-
 tests/test_meeg_io.m                              | 5 ++++-
 tests/test_meeg_layout_collection.m               | 5 ++++-
 tests/test_meeg_read_layout.m                     | 5 ++++-
 tests/test_meeg_senstype_collection.m             | 5 ++++-
 tests/test_meeg_source.m                          | 5 ++++-
 tests/test_montecarlo_cluster_stat.m              | 5 ++++-
 tests/test_montecarlo_cluster_stat_distribution.m | 5 ++++-
 tests/test_naive_bayes_classifier_searchlight.m   | 5 ++++-
 tests/test_neighborhood_split.m                   | 5 ++++-
 tests/test_normalize.m                            | 5 ++++-
 tests/test_oddeven_partitioner.m                  | 5 ++++-
 tests/test_parallel_get_nproc_available.m         | 5 ++++-
 tests/test_parcellfun.m                           | 5 ++++-
 tests/test_partitions.m                           | 5 ++++-
 tests/test_pca.m                                  | 5 ++++-
 tests/test_pdist.m                                | 5 ++++-
 tests/test_plot_slices.m                          | 5 ++++-
 tests/test_publish_run_scripts.m                  | 5 ++++-
 tests/test_rand.m                                 | 5 ++++-
 tests/test_randomize_targets.m                    | 5 ++++-
 tests/test_randperm.m                             | 5 ++++-
 tests/test_remove_useless_data.m                  | 5 ++++-
 tests/test_run_tests.m                            | 5 ++++-
 tests/test_sample_unique.m                        | 5 ++++-
 tests/test_searchlight.m                          | 5 ++++-
 tests/test_show_progress.m                        | 5 ++++-
 tests/test_slice.m                                | 5 ++++-
 tests/test_spherical_neighborhood.m               | 5 ++++-
 tests/test_split.m                                | 5 ++++-
 tests/test_squareform.m                           | 5 ++++-
 tests/test_stack.m                                | 5 ++++-
 tests/test_stat.m                                 | 5 ++++-
 tests/test_statcode.m                             | 5 ++++-
 tests/test_strjoin.m                              | 5 ++++-
 tests/test_strsplit.m                             | 5 ++++-
 tests/test_structjoin.m                           | 5 ++++-
 tests/test_surface_io.m                           | 5 ++++-
 tests/test_surficial_io_gifti.m                   | 5 ++++-
 tests/test_surficial_io_niml_dset.m               | 5 ++++-
 tests/test_surficial_neighborhood.m               | 5 ++++-
 tests/test_synthetic_dataset.m                    | 5 ++++-
 tests/test_tail.m                                 | 5 ++++-
 tests/test_target_dsm_corr_measure.m              | 5 ++++-
 tests/test_type.m                                 | 5 ++++-
 tests/test_vol_coordinates.m                      | 5 ++++-
 tests/test_vol_grid_convert.m                     | 5 ++++-
 tests/test_warning.m                              | 5 ++++-
 tests/test_wtf.m                                  | 5 ++++-
 108 files changed, 432 insertions(+), 104 deletions(-)

commit a19a8cef340b41a275f3885942462dee927d3bda
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jan 19 20:29:39 2017 +0100

    TST: add missing parenthesis

 tests/test_vol_coordinates.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 588fe8eb4f210c7e7e86cae2250c27055d13a1f6
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jan 19 20:29:26 2017 +0100

    SML: minor change in wording

 mvpa/cosmo_independent_samples_partitioner.m | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit 61cc07a302d248ff51c9a3f81f92ff04bc9ff980
Merge: 6d41023 f5e02a2
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Mon Jan 16 17:57:04 2017 +0100

    Merge pull request #127 from nno/hvidaldossantos-fix_cosmo_config
        ENH: make cosmo_config work with different path separators on
        Windows and Unix

commit f5e02a2313df59db1dc2da6d85893c1f042368ad
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Jan 16 17:11:23 2017 +0100

    ENH: make cosmo_config work with different path separators in
        Windows and Unix platforms

 mvpa/cosmo_config.m | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit e7379a3b7522d50a01b8b50c8299df2d941adbcc
Merge: 6d41023 1c12a6a
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Jan 16 17:09:05 2017 +0100

    Merge branch 'fix_cosmo_config' of
        https://github.com/hvidaldossantos/CoSMoMVPA into
        hvidaldossantos-fix_cosmo_config