_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]    2 bug fixes
  [BK]    3 changes that break existing functionality
 [BLD]    5 changes in build system
 [ENH]    4 enhancements
  [NF]    3 new features
[OCTV]    1 Octave-compatibility improvements
  [RF]    1 refactorings
 [SML]    2 minor changes
 [TST]    5 unit or doctest changes
 [WEB]    3 website documentation changes

Acknowledgements

- Moritz Wurm
- Tijl Grootswagers
- Yuan Tao

Changes that break existing functionality

commit 5edd5af7734e601f76c7bc92a368c0a8e16fb429
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jul 22 14:51:39 2016 +0200

    BLD+BK: temporarily disable 3 tests that involve Octave package
        "io" version 2.4.2, as these cause unexpected errors

 tests/test_run_tests.m | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

commit 83cd0250eb9f7368520e22db34d4895d2fdf5a1c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 30 17:19:17 2016 +0200

    BF+BK+ACK: fix wrong output when using
        cosmo_montecarlo_cluster_stat with both feature_stat=none and
        h0_mean=c for c~=0. As a result, output maps were biased,
        showing either too many negative [positive] clusters for
        positive [negative] values of c. Thanks to #Moritz Wurm# for
        asking a question about this

 mvpa/cosmo_montecarlo_cluster_stat.m |  3 ++-
 tests/test_montecarlo_cluster_stat.m | 22 ++++++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

Bug fixes

commit 83cd0250eb9f7368520e22db34d4895d2fdf5a1c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 30 17:19:17 2016 +0200

    BF+BK+ACK: fix wrong output when using
        cosmo_montecarlo_cluster_stat with both feature_stat=none and
        h0_mean=c for c~=0. As a result, output maps were biased,
        showing either too many negative [positive] clusters for
        positive [negative] values of c. Thanks to #Moritz Wurm# for
        asking a question about this

 mvpa/cosmo_montecarlo_cluster_stat.m |  3 ++-
 tests/test_montecarlo_cluster_stat.m | 22 ++++++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

All changes

commit 6953476d0677b56aa735bcf4f3a42acb63223510
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jul 22 16:48:07 2016 +0200

    WEB: add link to github

 doc/source/index.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 5479fe78a09adb45b5ae488d06d2592b8fa6964b
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jul 22 16:46:14 2016 +0200

    WEB: indicate that multiple platforms are supported

 doc/source/index.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit f2bbc27f64c94eeabde78b9ff82c45053e769e3d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jul 22 16:32:07 2016 +0200

    WEB: the CoSMoMVPA manuscript has been published. Yay!

 doc/source/faq.rst        | 8 ++++----
 doc/source/news.rst       | 4 ++--
 doc/source/references.bib | 4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

commit bdc2ea841c9ad5e097025a0761a95f17e2319dfe
Merge: f032f8a 5edd5af
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Jul 22 15:33:12 2016 +0200

    Merge pull request #78 from
        nno/_to_fix/failing_test_octave_io_2_4_2          BLD:
        fix/failing test octave io 2.4.2

commit 5edd5af7734e601f76c7bc92a368c0a8e16fb429
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Jul 22 14:51:39 2016 +0200

    BLD+BK: temporarily disable 3 tests that involve Octave package
        "io" version 2.4.2, as these cause unexpected errors

 tests/test_run_tests.m | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

commit 439a154bef4e443518c1f33128bfff1cec9fcd7c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Jul 19 15:18:41 2016 +0200

    SML: fix whitespace

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

commit f032f8a9885d30950f13480337f7200ce26f92c7
Merge: e6eeddc 8ee1778
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Jul 5 18:40:16 2016 +0200

    Merge pull request #75 from nno/_cmpt/isequaln          CMPT+NF:
        new function "cosmo_isequaln"

commit 8ee1778fc16e81a3e92f59d38a084bd0d062da50
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Jul 5 17:53:39 2016 +0200

    CMPT: introduce isequaln fetter support of older verions of Matlab
        (without isequaln) and future versions of GNU Octave (when
        isequalwithequalnans will be deprecated)

 mvpa/cosmo_align.m              |  2 +-
 mvpa/cosmo_check_neighborhood.m |  8 ++---
 mvpa/cosmo_isequaln.m           | 64 +++++++++++++++++++++++++++++++++++
 mvpa/cosmo_stack.m              |  2 +-
 tests/test_isequaln.m           | 75 +++++++++++++++++++++++++++++++++++++++++
 5 files changed, 145 insertions(+), 6 deletions(-)

commit e6eeddc393a6c29ca60cbf532e6f45f31a7e8953
Merge: 10b8bd0 61c8a04
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Jul 5 16:35:23 2016 +0200

    Merge pull request #74 from nno/_enh/niml_uniform_datatype
        ENH: use uniform datatype for NIML

commit d734a97ab397b7a356c146051b5d3cf2fabf9a4c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Jul 5 16:29:27 2016 +0200

    TST: use random data

 tests/test_montecarlo_cluster_stat.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

commit 10b8bd0692e0c6044bf54f0282174498ffd9df71
Merge: 0b5d85d b2c4fa4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Jul 5 15:53:26 2016 +0200

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

commit 0b5d85dc7ba00bf83e735bb36af3bf6f99717eb4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Jul 5 15:53:07 2016 +0200

    SML+RF: use different variable name

 mvpa/cosmo_warning.m | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

commit 61c8a046c57a76a424272a33b82f46ac41fea058
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Jul 5 15:52:09 2016 +0200

    ENH: use uniform datatype for NIML

 tests/test_surficial_io_niml_dset.m | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

commit b2c4fa4dd4b3430fed598975edce6f991a8903fa
Merge: 5345129 486af8d
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Jul 5 10:27:46 2016 +0200

    Merge pull request #73 from nno/_octv/parcoverage          BLD:
        parallel coverage computation

commit 486af8d2bb03f7e1780dbc0cd854baada9fa79a8
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Jul 4 17:37:34 2016 +0200

    BLD: add webhook

 .travis.yml | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

commit 986f9c60db9b243def9a34912d70a321937540c2
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Jul 4 17:19:20 2016 +0200

    BLD+TST: support for partitioning tests

 .travis.yml            | 10 ++++++++--
 Makefile               | 10 ++++++++++
 mvpa/cosmo_run_tests.m |  4 +++-
 3 files changed, 21 insertions(+), 3 deletions(-)

commit 5345129645b2fdeeb7ef14a798fb647bd1b2be97
Merge: 734688c 83cd025
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Thu Jun 30 17:31:25 2016 +0200

    Merge pull request #72 from
        nno/_bf/non_feature_stat_with_h0_mean_fix          BF+BK+ACK:
        fix wrong output when using cosmo_montecarlo_cluster_stat

commit 83cd0250eb9f7368520e22db34d4895d2fdf5a1c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 30 17:19:17 2016 +0200

    BF+BK+ACK: fix wrong output when using
        cosmo_montecarlo_cluster_stat with both feature_stat=none and
        h0_mean=c for c~=0. As a result, output maps were biased,
        showing either too many negative [positive] clusters for
        positive [negative] values of c. Thanks to #Moritz Wurm# for
        asking a question about this

 mvpa/cosmo_montecarlo_cluster_stat.m |  3 ++-
 tests/test_montecarlo_cluster_stat.m | 22 ++++++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

commit 734688ce0d002efe41f228112c6940220fcc08a4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 30 11:48:19 2016 +0200

    FAQ+ACK: add entry about balancing partitions. Thanks to #Tijl
        Grootswagers# and #Yuan Tao# for asking about this

 doc/source/faq.rst    | 13 +++++++++++++
 doc/source/thanks.rst |  1 +
 2 files changed, 14 insertions(+)

commit 0cdc18a792b0e413782ffbd356fc91f0f1065556
Merge: dfea8a4 7b864df
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Jun 29 18:02:42 2016 +0200

    Merge branch '__cmpt/octave-disable-warnings'

commit 7b864df902ba5b1a1d9ee3b04dc3931379bfe878
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 18:09:43 2016 +0200

    OCTV: disable certain warnings

 .travis.yml                   |  25 +++++-
 mvpa/cosmo_config.m           |   7 +-
 mvpa/cosmo_warning.m          | 187 ++++++++++++++++++++++++------------------
 tests/test_align.m            |   1 +
 tests/test_check_external.m   |  10 ++-
 tests/test_config.m           |   7 +-
 tests/test_external_surfing.m |   2 +-
 7 files changed, 142 insertions(+), 97 deletions(-)

commit f201dc3fd5fdcecf05a2dc822fee38e586d74619
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 17:00:12 2016 +0200

    CMPT: check for presence of fieldtrip

 tests/test_meeg_senstype_collection.m | 4 ++++
 1 file changed, 4 insertions(+)

commit f79ed7b0f99420bc4bbd62ba839b94edb0026917
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 16:48:15 2016 +0200

    CMPT: support recent FieldTrip versions that allow
        ft_senslabel('neuromag306_combined') (see FieldTrip bug 3144)

 mvpa/cosmo_meeg_senstype_collection.m | 64 ++++++++++++++++++++++++++++++++---
 tests/test_meeg_senstype_collection.m | 30 ++++++++++++++++
 2 files changed, 89 insertions(+), 5 deletions(-)

commit ea27fc9d6503eb0d57b7c6925970047932f0342d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 11:42:14 2016 +0200

    NF+TST: support a "warnings" argument

 mvpa/cosmo_run_tests.m | 18 ++++++++++++++++++
 mvpa/cosmo_wtf.m       | 11 +++++++++++
 tests/test_wtf.m       | 38 +++++++++++++++++++++++++++++++++-----
 3 files changed, 62 insertions(+), 5 deletions(-)

commit dfea8a41bed724514c754a95fee0813936fce7aa
Merge: 66d882e d754427
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Thu Jun 23 17:51:40 2016 +0200

    Merge pull request #69 from nno/_cmp/fieldtrip-changes-bug3144
        CMPT: support FieldTrip changes since bug3144

commit 66d882ec798d1bb1110810e85ad51ba8753d46d5
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 17:34:25 2016 +0200

    TST+ENH: always provide format identifier

 mvpa/cosmo_type.m | 3 ++-
 tests/test_type.m | 9 +++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

commit d754427f86744cc1820d5fb715848f58fbd16247
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 17:00:12 2016 +0200

    CMPT: check for presence of fieldtrip

 tests/test_meeg_senstype_collection.m | 4 ++++
 1 file changed, 4 insertions(+)

commit ae14136904ea5ae8336755834a7a22eeea772eb7
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 16:48:54 2016 +0200

    ENH: test for proper presence of evalc

 tests/test_type.m | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

commit ce9941970b2deaafc6cf17dbc448aa041916c1f2
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 16:48:15 2016 +0200

    CMPT: support recent FieldTrip versions that allow
        ft_senslabel('neuromag306_combined') (see FieldTrip bug 3144)

 mvpa/cosmo_meeg_senstype_collection.m | 64 ++++++++++++++++++++++++++++++++---
 tests/test_meeg_senstype_collection.m | 30 ++++++++++++++++
 2 files changed, 89 insertions(+), 5 deletions(-)

commit 9c99efda8bcbecb5247ec74a42b72efa14c4a558
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Jun 23 11:42:14 2016 +0200

    NF+TST: support a "warnings" argument

 mvpa/cosmo_run_tests.m | 18 ++++++++++++++++++
 mvpa/cosmo_wtf.m       | 11 +++++++++++
 tests/test_wtf.m       | 38 +++++++++++++++++++++++++++++++++-----
 3 files changed, 62 insertions(+), 5 deletions(-)

Indices and tables