_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

Changes since last month

Summary

[BLD]    5 changes in build system
[DOC]    4 code documentation changes
[ENH]    9 enhancements
[EXC]   10 exercise-related changes
 [NF]    1 new features
[SML]    1 minor changes
[TST]    2 unit or doctest changes
[WEB]   11 website documentation changes

All changes

commit 21389f4d20e1737bbff6d52bf2b2537bf669bb88
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Mar 25 10:59:45 2017 -0300

    EXC: add reference to Kaiser, Oosterhof and Peelen paper

 doc/source/ex_meeg_time_generalization.rst |  3 +++
 doc/source/references.bib                  | 11 ++++++++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

commit ecf012ad19abd2c04029421a70d12e92aab63e66
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 22 14:08:42 2017 -0300

    EXC+SML: fix typo

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

commit 60510ff5d9866d279dfcce7e12c53ea343ffe6bc
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 22 12:37:09 2017 -0300

    WEB: make labman2017 primary in exercises

 doc/source/documentation.rst   | 5 +++--
 doc/source/prni2016_ex_toc.rst | 3 +--
 doc/source/rhul2016_ex_toc.rst | 1 -
 3 files changed, 4 insertions(+), 5 deletions(-)

commit 7b72c07676e369c80e3407fba0d63dcdff3d06df
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 22 11:43:13 2017 -0300

    EXC: add warning to double dipping exercise

 examples/run_bad_double_dipping_analysis.m | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

commit 6d5bb3f1c666f4cbe6bc4fe896ac20901a75bd8a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 22 11:21:26 2017 -0300

    EXC: add warning for double dipping analysis

 examples/run_bad_double_dipping_analysis.m | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

commit b45a2edd48c93318f0a31be2b5b72f67dd3e1c4f
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 22 10:30:47 2017 -0300

    EXC: use better variable name for test data

 examples/run_bad_double_dipping_analysis.m | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

commit 1e729e19190267d9b0bcfc2b9e38f9c0c34347b4
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Mar 21 17:57:24 2017 -0300

    WEB: revert back to original schedule

 doc/source/labman2017_intro.rst | 5 +----
 doc/source/news.rst             | 2 +-
 2 files changed, 2 insertions(+), 5 deletions(-)

commit e538dea76f36c68e4b09f305e478043c57249ab9
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Mar 21 16:04:27 2017 -0300

    EXC: clarify what is to be computed

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

commit de36799e670d3712dd2dd8e481b6a1da393d8fff
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Mar 21 14:53:29 2017 -0300

    WEB: fix git merge conflict

 doc/source/labman2017_intro.rst | 5 -----
 1 file changed, 5 deletions(-)

commit b22b17101809678a5bf682e0f21bc0f404832f45
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 21 14:38:31 2017 -0300

    BLD: use hydra

 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 6cd8e83073c1645c9017c1e5923493b0dd95b25b
Merge: 2042e93 e4e910c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 21 14:37:50 2017 -0300

    MRG: resolve merge conflict

commit 2042e93b6cc617f1246247c4c5a2027bd3af0553
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 21 14:35:25 2017 -0300

    WEB: update schedule

 doc/source/labman2017_intro.rst | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

commit e4e910c7ba9957915bf7ea965adc7914a30be37d
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 21:55:47 2017 -0300

    WEB: update info for LABMAN

 doc/source/download.rst       | 8 ++++++--
 doc/source/labman2017.rst     | 6 +++---
 doc/source/quick_download.txt | 4 ++--
 3 files changed, 11 insertions(+), 7 deletions(-)

commit f93922b9568057eb82b25bfce74bdbac2085dfcc
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 20:39:17 2017 -0300

    WEB: add meeting point

 doc/source/labman2017_intro.rst | 2 ++
 1 file changed, 2 insertions(+)

commit e3d983365d9f1c5c8871a02391c7ba0116c4da6a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 12:25:41 2017 -0300

    DOC: add explanation about time-freq searchlight

 doc/source/ex_meeg_searchlight.rst | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

commit 1be590f9d60b0da65b02acd7f7993d9a195d84fa
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 12:11:31 2017 -0300

    EXC: new time-freq exercise

 examples/run_meeg_timefreq_measures.m | 206 ++++++++++++++++++++++++++++++++++
 1 file changed, 206 insertions(+)

commit e21ed321d2ff28cb6c59edd0c8d72bf82aeaa80d
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 12:10:59 2017 -0300

    DOC: remove part about chunk caveat as it does no longer apply

 examples/run_meeg_time_generalization.m | 5 +----
 examples/run_meeg_timelock_measures.m   | 5 +----
 2 files changed, 2 insertions(+), 8 deletions(-)

commit 5be777caa6a4362de5572ffaf4e66a5c0684ebe9
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 12:10:17 2017 -0300

    WEB: link to full dataset

 doc/source/labman2017_intro.rst | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

commit 7a9c75a9ab0a43516e89e694db9a0491157457a2
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Mar 19 11:27:13 2017 -0300

    BLD: use proper rsync directory for indirect sync

 Makefile | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

commit 457f8f0233429e5056a3b38be929f4bbc10aff47
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sat Mar 18 20:22:54 2017 -0300

    MSC: revert back to original FieldTrip as the issue causing Octave
        to throw an error has been fixed

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 78df796fae5443115a350a4fdb4caf9c12517bb0
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sat Mar 18 20:21:46 2017 -0300

    EXC: new exercise about double dipping

 doc/source/ex_classify_double_dipping.rst  | 33 ++++++++++++++++
 doc/source/labman2017_ex_toc.rst           |  2 +
 examples/run_bad_double_dipping_analysis.m | 60 ++++++++++++++++++++++++++++++
 3 files changed, 95 insertions(+)

commit feb8b36d6433db05e0247fabf455e071f89f9790
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sat Mar 18 19:05:54 2017 -0300

    BLD: simplify making run scripts

 mvpa/cosmo_publish_run_scripts.m | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

commit c6979e8b8926a6f68c377adc26c361aeb64b63d4
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 14:42:10 2017 -0300

    WEB: descibe using pip

 doc/source/contribute.rst | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

commit 149db268a8f7c2ff7be7e06ae9ada693d780f2df
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 14:33:07 2017 -0300

    ENH: show reassuring message

 examples/cosmo_wizard_set_config.m | 1 +
 1 file changed, 1 insertion(+)

commit 014c762006582f2746170b54441e05a75a50cc3b
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Mar 15 14:17:39 2017 -0300

    BLD: Makefile for LABMAN

 Makefile | 55 ++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 48 insertions(+), 7 deletions(-)

commit 705b29537bafb0d2b8eb5c103f2ffd7b0cff1cf4
Merge: 751d452 de3eba3
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 12:42:49 2017 -0300

    Merge pull request #137 from nno/_enh/compat_norminv          ENH:
        norminv

commit de3eba3c7da3bb464ff8e4b525602c6206722265
Merge: ed63a91 751d452
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 09:45:41 2017 -0300

    Merge branch 'master' into _enh/compat_norminv

commit 751d452736cbe281e59bb6b5a097fee8f749e96d
Merge: e681013 af691d1
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 09:45:20 2017 -0300

    Merge pull request #138 from nno/_compat/isequaln          ENH:
        use cosmo_isequaln everywhere

commit ed63a91f0c457faefc6f8cfe83fe01f459bf2a6a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 09:18:22 2017 -0300

    ENH: do not try non-scalar inputs with Octave

 tests/test_norminv.m | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

commit af691d1ca274a111f8078662fba504ca80befce0
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 07:54:47 2017 -0300

    TF: do not use cosmo_cosmo_ function because it does not exist

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

commit 716c862562aeb21cb99a5e713e24fa7b2ff083e0
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 07:49:50 2017 -0300

    TST: switch off warning message

 tests/test_searchlight.m | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

commit 3b73005d4b6e6129d21803784c1cb90865877c1a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 07:45:01 2017 -0300

    ENH: always use cosmo_norminv, not norminv

 mvpa/cosmo_montecarlo_cluster_stat.m              | 4 ++--
 mvpa/cosmo_stat.m                                 | 6 +-----
 mvpa/cosmo_synthetic_dataset.m                    | 2 +-
 tests/test_meeg_io.m                              | 2 +-
 tests/test_montecarlo_cluster_stat_distribution.m | 4 ----
 5 files changed, 5 insertions(+), 13 deletions(-)

commit 3969b3da3a4109a5f9566264ef30876f8c70a74c
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 07:38:58 2017 -0300

    ENH: use cosmo_isequaln everywhere

 mvpa/cosmo_align.m              | 2 +-
 mvpa/cosmo_check_neighborhood.m | 8 ++++----
 mvpa/cosmo_squareform.m         | 2 +-
 mvpa/cosmo_stack.m              | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

commit c59ae7991407ddeaf371bc9f9d9625e0f4b7bbbe
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Mar 15 07:35:45 2017 -0300

    NF: norminv function

 mvpa/cosmo_norminv.m | 35 +++++++++++++++++++++++++++++++++++
 tests/test_norminv.m | 44 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)

commit e68101386a9c4e4048f2e9684e867512ade9ea88
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 14 08:42:52 2017 +0100

    WEB: add link to LABMAN in news

 doc/source/news.rst | 1 +
 1 file changed, 1 insertion(+)

commit a9405bc0544503a1e506afccf740e4d6a1046a7b
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 14 07:51:49 2017 +0100

    BLD: add "remote" target in Makefile

 Makefile | 2 ++
 1 file changed, 2 insertions(+)

commit fe058c5c1a01d344552bfec099b9f3e71c5ec10f
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 14 07:46:33 2017 +0100

    EXC: use independent samples partitioner

 examples/run_meeg_timelock_measures.m | 48 ++++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 20 deletions(-)

commit 53ef050e26ca1a59c234f380b803fd2bd98f5b2f
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Mar 14 07:45:52 2017 +0100

    WEB: add LABMAN 2017

 doc/source/all_exercises_ever_toc.txt |   1 +
 doc/source/index.rst                  |   4 +-
 doc/source/labman2017.rst             |  57 ++++++++++++
 doc/source/labman2017_ex_toc.rst      |  32 +++++++
 doc/source/labman2017_intro.rst       | 170 ++++++++++++++++++++++++++++++++++
 doc/source/links.txt                  |   1 +
 6 files changed, 263 insertions(+), 2 deletions(-)

commit 930a728c1c9be4d59b55adbe4333ebb82ea23ab8
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Mar 13 18:19:30 2017 +0100

    WEB: update links

 doc/source/cimec2016_intro.rst | 4 ++--
 doc/source/download.rst        | 9 +++++----
 doc/source/prni2016_intro.rst  | 4 ++--
 doc/source/quick_download.txt  | 9 ++++-----
 4 files changed, 13 insertions(+), 13 deletions(-)

commit 02f3edbc9f2a2e7af99e81a6c4f30a23ee86fb6e
Merge: 6e42812 6da97fb
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Mon Mar 13 13:10:29 2017 +0100

    Merge pull request #136 from nno/_msc/use_custom_fieldtrip
        FIX: temporarily skip using official FieldTrip because it
        makes the build crash

commit 6da97fb645c257274d6e63ff2ccf34aea40cd572
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Mar 13 12:13:40 2017 +0100

    FIX: temporarily skip using official FieldTrip because it makes
        the build crash. Issue reported at
        http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3269

 .travis.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

commit 6e4281262eef7a52b792675281da615cd5bddf56
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Mar 12 20:27:21 2017 +0100

    DOC: describe handling multiple partitions in more detail

 mvpa/cosmo_independent_samples_partitioner.m | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

commit 7cb952a25be7de3f28bc567c23d728d2f6bdf674
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Mar 12 20:26:46 2017 +0100

    EXC: assign accuracy

 examples/run_cross_validation.m | 1 +
 1 file changed, 1 insertion(+)

commit c0a866c93eafd1ff41b4a95ed27a0d8d544a447b
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Mar 12 20:26:29 2017 +0100

    ENH: use onCleanup when opening file

 examples/cosmo_wizard_set_config.m | 3 +++
 1 file changed, 3 insertions(+)

commit 8b7b2c438af73f48e581450257e8bf65361daed6
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Mar 6 11:27:18 2017 +0100

    DOC: minor tweaks to documentation

 mvpa/cosmo_balance_partitions.m | 33 +++++++++++++++++++--------------
 1 file changed, 19 insertions(+), 14 deletions(-)

commit 64c5e1706038cc2f89b28da9fca9e8de71081806
Merge: b67d1d2 1b8f9c7
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sat Mar 4 12:01:40 2017 +0100

    Merge pull request #135 from nno/_enh/catch_error_pool
        ENH: do not throw error when unable to start parallel pool

commit 1b8f9c731ae387d71200c314b06f96ec0f9d2af5
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Mar 3 18:29:25 2017 +0100

    TST: skip test with non-matching Matlab versions

 tests/test_parallel_get_nproc_available.m | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

commit 73e6874d25e0ef5f1fd032311c1561ba8cdf9286
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Mar 3 17:52:05 2017 +0100

    ENH: do not throw error when unable to start parallel pool

 mvpa/cosmo_parallel_get_nproc_available.m | 34 ++++++++++++++++++++-----------
 tests/test_parallel_get_nproc_available.m | 33 ++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+), 12 deletions(-)