_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

[BLD]    1 changes in build system
[CLN]    1 clean-ups
[DOC]    2 code documentation changes
[ENH]    8 enhancements
 [NF]    7 new features
[OPT]    1 optimizations
 [RF]    1 refactorings
[SML]    1 minor changes
[TST]    5 unit or doctest changes

Acknowledgements

- Tijl Grootswagers
- Evelyn Muschter

All changes

commit 33b68e4616a5472ac3a7a210281dadf7fdde2383
Merge: b181a06 778baa4
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Sep 12 22:45:44 2017 +0200

    Merge pull request #163 from nno/_enh/meeg_source_without_dim
        ENH+ACK: add support for FieldTrip MEEG data structures
        without "dim" field

commit 778baa4eb06da93054ba50d68397dd91b5e7d8ae
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Sep 12 18:54:14 2017 +0200

    CLN: remove unused commented-out code

 mvpa/cosmo_map2meeg.m | 7 -------
 1 file changed, 7 deletions(-)

commit 191fea3151b2fd2fde18a1e9f434267403521a28
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Sep 12 18:52:41 2017 +0200

    ENH+ACK: add support for FieldTrip MEEG data structures without
        "dim" field. Issue reported by #Evelyn Muschter#

 mvpa/cosmo_map2meeg.m     | 16 ++++++++++------
 mvpa/cosmo_meeg_dataset.m | 18 +++++++++++++++---
 tests/test_meeg_io.m      | 48 +++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 73 insertions(+), 9 deletions(-)

commit b181a06e8ce4c0993615ff47418ad835f07c651f
Merge: acf66fb c345d65
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Aug 22 12:34:18 2017 +0200

    Merge pull request #162 from nno/Tijl-test_partial_spearman
        NF: Support for partial Spearman correlations in
        cosmo_target_dsm_corr_measure

commit c345d65dba0c1882008a213744795fc970241c0f
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Aug 22 09:46:40 2017 +0200

    ENH+TST+DOC: more strict test on when using Kendall as correlation
        type, allowing it for simple correlations but not with glm or
        regress matrices

 mvpa/cosmo_target_dsm_corr_measure.m | 23 +++++++++++++++--------
 tests/test_target_dsm_corr_measure.m |  8 ++++++--
 2 files changed, 21 insertions(+), 10 deletions(-)

commit e786074465eb3737e1b6365ab87ab842ebeb0677
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Aug 22 09:32:47 2017 +0200

    ENH: remove unused default parameter

 mvpa/cosmo_target_dsm_corr_measure.m | 1 -
 1 file changed, 1 deletion(-)

commit 271cb8b082e01c24128aad9b7535ab8fa6f2c3e5
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Aug 21 13:48:56 2017 +0200

    DOC: clarify use of "type" parameter

 mvpa/cosmo_target_dsm_corr_measure.m | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

commit a2c99e99ae652f25b932168bb3bdda62d60b3ba0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Aug 21 13:42:17 2017 +0200

    ENH: throw error when using glm_dsm with other correlation type
        than Pearson

 mvpa/cosmo_target_dsm_corr_measure.m | 4 ++++
 tests/test_target_dsm_corr_measure.m | 2 ++
 2 files changed, 6 insertions(+)

commit 4dce97bf29a079e89ffc9fe7d007268580b7e1b1
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Aug 21 13:36:43 2017 +0200

    ENH: use "type", not "partial_type", when computing partial
        correlation

 mvpa/cosmo_target_dsm_corr_measure.m | 17 ++++++++---------
 tests/test_target_dsm_corr_measure.m |  8 ++------
 2 files changed, 10 insertions(+), 15 deletions(-)

commit f17ace0c78fe8bdf57a9d5656af782f1231a8649
Merge: 49a302d acf66fb
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 17:02:15 2017 +0200

    Merge branch 'master' into Tijl-test_partial_spearman

commit acf66fb40a084217ea13e77a93fca238b1acd08f
Merge: 6e71de4 b085a32
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Aug 20 17:01:36 2017 +0200

    Merge pull request #161 from nno/_nf/spearman_corr          NF:
        support for Spearman correlation in cosmo_corr

commit 49a302d8ab09b747a057326c0f0f28316924869e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:55:45 2017 +0200

    NF+ENH+ACK: add support for partial Spearman correlations with the
        new "partial_type" argument. Thanks to #Tijl Grootswagers# for
        reporting the issue of missing functionality and providing a
        useful test case

 mvpa/cosmo_target_dsm_corr_measure.m | 34 +++++++++++++++++++++++++++-------
 tests/test_target_dsm_corr_measure.m |  7 +++++--
 2 files changed, 32 insertions(+), 9 deletions(-)

commit edd79fa231bb7994f7a90c16de4e9c4ec9581027
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:53:30 2017 +0200

    TST: enable accidentally disabled tests

 tests/test_target_dsm_corr_measure.m | 8 --------
 1 file changed, 8 deletions(-)

commit 1b945fa26357d61b1022229007f68f38b3a2bd1a
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:52:57 2017 +0200

    TST: revert back earlier change of output value for Spearman
        correlation

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

commit f8302d3798f4e83af343051f6f65de7f0531fc3b
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:39:35 2017 +0200

    ENH: more stringent test for correlation type argument

 mvpa/cosmo_target_dsm_corr_measure.m | 8 ++++++--
 tests/test_target_dsm_corr_measure.m | 4 ++++
 2 files changed, 10 insertions(+), 2 deletions(-)

commit 6ab58551dfab29ad4fb997558619eed4bcab1245
Merge: 9bfe0b4 6e71de4
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:34:26 2017 +0200

    Merge branch 'master' into Tijl-test_partial_spearman

commit 6e71de4edb2906326ef894ecd2faef2f5ec6d582
Merge: 2c9b68e a51ce29
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Aug 20 16:33:52 2017 +0200

    Merge pull request #160 from nno/_nf/tiedrank          NF:
        cosmo_tiedrank

commit 9bfe0b4934b99e2cb23d2f62713c2f88f8f57727
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:33:15 2017 +0200

    TST: update test to reflect the same value as returned by Matlab's
        partialcorr function

 tests/test_target_dsm_corr_measure.m | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

commit b085a32bb1d59e8efe7e4973d6b658a298cc1326
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:03:16 2017 +0200

    NF: support Spearman correlation directly

 mvpa/cosmo_corr.m | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

commit 3ba1888c8fa638421be2ff4399a779448e7ad779
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 16:00:26 2017 +0200

    RF: use helper functon for Pearson correlation

 mvpa/cosmo_corr.m | 53 +++++++++++++++++++++++++++++------------------------
 1 file changed, 29 insertions(+), 24 deletions(-)

commit 8d014bceba85dff57a56d98608f9878838fc4234
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 15:58:19 2017 +0200

    TST: add regression tests for Spearman and Pearson correlations

 tests/test_corr.m | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

commit a51ce29a28944d7165f05f571cade47ba99859d0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 15:35:11 2017 +0200

    SML: remove whitespace

 mvpa/cosmo_tiedrank.m | 6 ------
 1 file changed, 6 deletions(-)

commit ab3dde92fa38031485c622dd66f65551db082db0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 15:33:38 2017 +0200

    OPT: faster implementation of tiedrank

 mvpa/cosmo_tiedrank.m | 49 +++++++++++++++++++++++++++++--------------------
 1 file changed, 29 insertions(+), 20 deletions(-)

commit 8a99e94c10303111787a95ac36d9fb54cdd8eaa0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Aug 20 14:57:37 2017 +0200

    NF: cosmo_tiedrank

 mvpa/cosmo_tiedrank.m | 154 ++++++++++++++++++++++++++++++++++++
 tests/test_tiedrank.m | 210 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 364 insertions(+)

commit 84b83a64a8cb1337b9defe8c35d4731f2513df43
Author: Tijl Grootswagers <t.grootswagers@gmail.com>
Date:   Thu Aug 17 13:15:44 2017 +1000

    Add spearman partial test

 tests/test_target_dsm_corr_measure.m | 12 ++++++++++++
 1 file changed, 12 insertions(+)

commit 8bcf3637070cbdd480c6c1b2e7193d5ebfb5b15f
Merge: 30a38fc 2c9b68e
Author: Tijl Grootswagers <t.grootswagers@gmail.com>
Date:   Thu Aug 17 13:10:30 2017 +1000

    Merge remote-tracking branch 'CoSMoMVPA/master'

commit 2c9b68ee8055ea625a2140d8741043bf71475d8c
Merge: 3ed6e43 0e1fc59
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Aug 15 15:47:09 2017 +0200

    Merge pull request #153 from nno/_nf/singleton_neighborhood
        NF: add support for singleton neighborhood for ROI analysis
        with MCC

commit 0e1fc598f9dc4321480a82150b495bc35d19cf2a
Merge: 0f7bb90 3ed6e43
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Aug 15 11:56:03 2017 +0200

    Merge branch 'master' into _nf/singleton_neighborhood

commit 3ed6e4324585324a7587f7b04b41471fe5f1e74c
Merge: edb9e92 ab31fc6
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Aug 15 11:41:50 2017 +0200

    Merge pull request #157 from nno/_tst/disable_parallel
        BLD: disable Octave parallel package