_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]    5 bug fixes
 [BIG]    3 major changes
  [BK]    1 changes that break existing functionality
 [BLD]    8 changes in build system
 [DOC]    5 code documentation changes
 [ENH]    5 enhancements
 [EXC]    1 exercise-related changes
  [NF]    6 new features
[OCTV]    1 Octave-compatibility improvements
 [OPT]    4 optimizations
  [RF]    7 refactorings
 [SML]    2 minor changes
 [TST]   26 unit or doctest changes
 [WEB]    8 website documentation changes

Acknowledgements

- Tijl Grootswagers
- Daria Proklova

Major changes

commit 7139bd0841451d9b6a285cc4a7a0a571617349ee
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Nov 27 17:53:22 2016 +0100

    BF+BIG: fix issue with very weak effects that may appear to be
        significant when using montecarlo_cluster_stat. This bug was
        introduced in commit ee50b05dfea0679e28a8ea5214fe02ae4f937745

 mvpa/cosmo_montecarlo_cluster_stat.m |  4 ++--
 tests/test_montecarlo_cluster_stat.m | 20 ++++++++++----------
 2 files changed, 12 insertions(+), 12 deletions(-)

commit 4e5113ddba00dc91c1004e08dc6d2f026bb8a71d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Nov 24 14:11:28 2016 +0100

    BF+BIG+BK: fix p-value and z-score computation; previous versions
        returned one-tailed instead of two-tailed z-scored,
        effectively doubling the type-I error rate

 mvpa/cosmo_montecarlo_cluster_stat.m              |  12 ++-
 tests/test_montecarlo_cluster_stat.m              |  73 ++++++++++---
 tests/test_montecarlo_cluster_stat_distribution.m | 124 ++++++++++++++++++++++
 3 files changed, 192 insertions(+), 17 deletions(-)

Changes that break existing functionality

commit 4e5113ddba00dc91c1004e08dc6d2f026bb8a71d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Nov 24 14:11:28 2016 +0100

    BF+BIG+BK: fix p-value and z-score computation; previous versions
        returned one-tailed instead of two-tailed z-scored,
        effectively doubling the type-I error rate

 mvpa/cosmo_montecarlo_cluster_stat.m              |  12 ++-
 tests/test_montecarlo_cluster_stat.m              |  73 ++++++++++---
 tests/test_montecarlo_cluster_stat_distribution.m | 124 ++++++++++++++++++++++
 3 files changed, 192 insertions(+), 17 deletions(-)

Bug fixes

commit 7139bd0841451d9b6a285cc4a7a0a571617349ee
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Nov 27 17:53:22 2016 +0100

    BF+BIG: fix issue with very weak effects that may appear to be
        significant when using montecarlo_cluster_stat. This bug was
        introduced in commit ee50b05dfea0679e28a8ea5214fe02ae4f937745

 mvpa/cosmo_montecarlo_cluster_stat.m |  4 ++--
 tests/test_montecarlo_cluster_stat.m | 20 ++++++++++----------
 2 files changed, 12 insertions(+), 12 deletions(-)

commit 4e5113ddba00dc91c1004e08dc6d2f026bb8a71d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Nov 24 14:11:28 2016 +0100

    BF+BIG+BK: fix p-value and z-score computation; previous versions
        returned one-tailed instead of two-tailed z-scored,
        effectively doubling the type-I error rate

 mvpa/cosmo_montecarlo_cluster_stat.m              |  12 ++-
 tests/test_montecarlo_cluster_stat.m              |  73 ++++++++++---
 tests/test_montecarlo_cluster_stat_distribution.m | 124 ++++++++++++++++++++++
 3 files changed, 192 insertions(+), 17 deletions(-)

commit 40b4f06c51631d736b6d988b13099ef56ddd42fb
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 21 13:33:53 2016 +0100

    BF: make cosmo_check_external return false for Octave package that
        is available but not loaded

 mvpa/cosmo_check_external.m | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

All changes

commit 032686f52def8c4afe0d16b2a318a5fae4cf5f3c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Dec 6 11:54:41 2016 +0100

    MSC: add Changelog, preparing for release v1.1.0

 Changelog                    | 65 ++++++++++++++++++++++++++++++++++++++++++++
 README.rst                   |  3 +-
 doc/source/changelog.rst     | 11 ++++++++
 doc/source/documentation.rst |  1 +
 doc/source/faq.rst           |  2 ++
 5 files changed, 81 insertions(+), 1 deletion(-)

commit 36d109e1b26a4937683fbef929616cbbfeb8c940
Merge: 1f30c0e f588a43
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Dec 6 11:06:53 2016 +0100

    Merge pull request #120 from nno/_enh/nchoosek_lower_limit
        ENH: do not explicitly compute nchoosek when the output is
        large

commit 1f30c0e5413b7721e1ed498c164f200814067eea
Merge: ecd9b10 24607a8
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Mon Dec 5 13:42:51 2016 +0100

    Merge pull request #121 from nno/_tst/mccs_more_sign_test
        TST: test using positive and negative sign

commit 24607a8a3cd5204cb1186cb63125c171375afb16
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Dec 5 13:05:31 2016 +0100

    TST: test using positive and negative sign

 tests/test_montecarlo_cluster_stat.m | 32 +++++++++++++++++++++++---------
 1 file changed, 23 insertions(+), 9 deletions(-)

commit f588a4361826e3127a7b379c4c6775973634c571
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Dec 5 11:49:08 2016 +0100

    ENH: do not explicitly compute nchoosek when the output is large

 mvpa/cosmo_independent_samples_partitioner.m | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

commit ecd9b10266d64f31aa3b2de64a90a229a57a0acf
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Dec 5 11:18:19 2016 +0100

    ENH: reduce memory usage when loading MEEG data

 mvpa/cosmo_meeg_dataset.m | 7 ++++++-
 tests/test_meeg_io.m      | 2 --
 2 files changed, 6 insertions(+), 3 deletions(-)

commit 77eeb5ed7badc11894bca40fad4181cff60019e6
Merge: c04df2a 5056c0f
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Dec 3 16:10:51 2016 +0100

    Merge branch '_tst/meeg_baseline'

commit 5056c0fc36a052b179a89b4504d0ffa349eebe49
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Dec 3 15:46:37 2016 +0100

    ENH: show error when .fa do not match for input and reference
        dataset

 mvpa/cosmo_meeg_baseline_correct.m | 28 +++++++++++-----------------
 tests/test_meeg_baseline_correct.m | 31 ++++++++++++++++++++++++++++++-
 2 files changed, 41 insertions(+), 18 deletions(-)

commit c04df2a44362c3a92a3c58fe39bef9a5bf8809f1
Merge: 056e535 165604b
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sat Dec 3 15:22:38 2016 +0100

    Merge pull request #119 from nno/_tst/meeg_baseline          TST:
        more tests for random data for MEEG baseline correction

commit 165604b7322435f88d02d58d51621177e7ef7bd7
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sat Dec 3 10:18:45 2016 +0100

    DOC: clarify "trials" option

 mvpa/cosmo_meeg_dataset.m | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

commit 7736b59d0959d27b345a825b9a716e66c3f5cae2
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Dec 2 16:26:20 2016 +0100

    TST: more tests for random data for MEEG baseline correction

 tests/test_meeg_baseline_correct.m | 153 +++++++++++++++++++++++++++++--------
 1 file changed, 121 insertions(+), 32 deletions(-)

commit 056e53567c6c0529df513682f4eeb4ccb80f5865
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 17:58:36 2016 +0100

    BLD: support "make clean" in root Makefile

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

commit cc5a79943e33e73af991efc6e4df09349711bd24
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 17:58:18 2016 +0100

    EXC: update exercise to reflect 3D structure of confusion matrix
        output

 examples/run_cross_validation.m | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

commit 3ce8aca6255b1f1ab977c9a4f2b288bafb17e453
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 17:22:32 2016 +0100

    TST: give a bit more signal

 tests/test_montecarlo_cluster_stat.m | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

commit 025de49b3592088ef52d189bb9b5a2a9d57097c6
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 16:51:02 2016 +0100

    MSC: update confusion matrix to reflect 3D output from
        cosmo_crossvalidate

 examples/demo_fmri_rois.m | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

commit e67c912e30c76200a492ad5f7ed3c57c39f8db13
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 16:14:07 2016 +0100

    WEB: ignore new matindex files

 doc/.gitignore | 1 +
 1 file changed, 1 insertion(+)

commit 1eff365c3d5751f07e00136ae39deb16e9dd9052
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:59:31 2016 +0100

    WEB+SML: fix typo

 doc/tools/matlab2rst.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit f5e65b94afbc399ce814dc50f509998d05faad7c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:59:16 2016 +0100

    WEB: add missing comma to separate two entries

 doc/tools/matlab2rst.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 7afa515e75b1487d9896ad474a43b4a86da40989
Merge: 69e7700 991298a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Thu Dec 1 14:53:36 2016 +0100

    Merge pull request #118 from nno/_web/fix_links          WEB: fix
        links on webpage

commit 991298a0f79158c8e32a00bd58c130572edf957c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:51:06 2016 +0100

    BLD: sort functions by name in module index

 doc/tools/matlab2rst.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 20d439062cd4d6be0480688957cfb099d3468c62
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:50:51 2016 +0100

    BLD: add parallel functions to index

 doc/tools/matlab2rst.py | 2 ++
 1 file changed, 2 insertions(+)

commit 1ba5ced79dc980310f019f922e2537eac384ef30
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:43:51 2016 +0100

    WEB+BLD: update index building script so that link labels come
        immediately before the title header

 doc/tools/matlab2rst.py | 34 +++++++++++++++++++++++++---------
 1 file changed, 25 insertions(+), 9 deletions(-)

commit 2ed64715b2c020ba7d6c36a3f3911669153605b9
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:42:59 2016 +0100

    WEB+ACK: fix dead links on website. Thanks to #Tijl Grootswagers#
        for reporting the issue

 doc/source/cimec2014.rst         | 16 ++++++++--------
 doc/source/cimec2016.rst         | 16 ++++++++--------
 doc/source/contribute.rst        |  2 +-
 doc/source/cosmo2013.rst         | 16 ++++++++--------
 doc/source/ex_dataset_basics.rst |  2 +-
 doc/source/ex_searchlight.rst    |  2 --
 doc/source/get_started.rst       |  4 ++--
 doc/source/index.rst             |  6 +++---
 doc/source/prni2016.rst          | 16 ++++++++--------
 doc/source/rhul2016.rst          | 16 ++++++++--------
 10 files changed, 47 insertions(+), 49 deletions(-)

commit 593663c538a9782caa4d4208040fdabe0c4c019d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:09:30 2016 +0100

    WEB: remove unsupported characters after link declaration

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

commit 3497f0b34c42740e95a3835f149f896e76813ddb
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Dec 1 14:08:42 2016 +0100

    BLD: support references on website using python Text class with
        .parts attribute

 doc/source/conf.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

commit e8369cc00a9bc2eeaf14625221b290ddeb4f56d6
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Nov 30 10:31:03 2016 +0100

    DOC+TST: update example output

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

commit 69e77009150d2dc44b54ad650c43200f434d77d5
Merge: 6071abe 84d3ff3
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Nov 29 12:58:51 2016 +0100

    Merge pull request #116 from nno/_tst/mccs_sign_correspondence
        TST: test for sign correspondence in monte carlo cluster
        statistics

commit 84d3ff3153759dca89384957dd598c9916b8d3b9
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 29 11:00:28 2016 +0100

    SML: remove whitespace

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

commit 7332ed412fcb9f2e23901828fdfba9f98c1d8cd5
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 29 10:59:45 2016 +0100

    TST: split up test in four parts

 tests/test_montecarlo_cluster_stat.m | 184 +++++++++++++++++++----------------
 1 file changed, 98 insertions(+), 86 deletions(-)

commit 97d750d28f96b51dc7081b585d5de23630ea1989
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 29 10:24:44 2016 +0100

    RF+TST: split tests in multiple parts

 tests/test_montecarlo_cluster_stat.m | 151 +++++++++++++++++++++++++++--------
 1 file changed, 116 insertions(+), 35 deletions(-)

commit b9195dbde7ed3edf38a39bac22e1f75981c0634c
Merge: 33ad07e 6071abe
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 18:11:31 2016 +0100

    MRG: resolve merge conflict

commit 6071abe8901f7e1e7805867c80bbe37350b0d6ea
Merge: a00372e 07ebb82
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Mon Nov 28 18:07:47 2016 +0100

    Merge pull request #117 from nno/_tst/progress_flush_mccs
        TST: remove progress string when done

commit 07ebb8275cb501a677d31863834d0757687cd18f
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 16:09:22 2016 +0100

    TST: do not show intermediate values

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

commit be84adf664047b94faafcf8d1172b0f7b6c0b032
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 16:08:31 2016 +0100

    TST: faster test for passing cases

 tests/test_montecarlo_cluster_stat_distribution.m | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

commit a5d7f8abf46ab06a9a957969d0dcdcb39646b1af
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 15:27:51 2016 +0100

    TST+OCTV: do not print newine character so that backspace printing
        removes all characters

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

commit 71c564b4a6b2f83ea23e725699ee242c7ca00743
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 15:25:00 2016 +0100

    TST: better show progress

 tests/test_montecarlo_cluster_stat_distribution.m | 40 ++++++++++-------------
 1 file changed, 18 insertions(+), 22 deletions(-)

commit dda1c6e06c06a23d46f29858215d3f7076d220a5
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 14:19:05 2016 +0100

    TST: remove progress string when done

 tests/test_montecarlo_cluster_stat_distribution.m | 33 +++++++++++++++++------
 1 file changed, 25 insertions(+), 8 deletions(-)

commit 33ad07eab02aabc5dfa525cba8fb200c7cda4599
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 13:47:04 2016 +0100

    TST: test for sign correspondence in monte carlo cluster
        statistics

 tests/test_montecarlo_cluster_stat.m | 135 +++++++++++++++++++++++++++++++----
 1 file changed, 121 insertions(+), 14 deletions(-)

commit 9daa1d7ed316ca6c05bd2529341090a3cae03d93
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 28 10:52:09 2016 +0100

    TST: fix typo in test name

 tests/test_montecarlo_cluster_stat_distribution.m | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

commit a00372ef52bb92e7a529db73ca0043c7544cb1ad
Merge: 2a8540a ad46d0c
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Nov 27 22:03:00 2016 +0100

    Merge pull request #114 from nno/_tst/test_mcct_distribution
        TST: show progress instead of skipping test when on CI
        platform

commit 2a8540af7532431bd14cdf52dad2f75c7b991eac
Merge: ee50b05 7139bd0
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Nov 27 18:27:55 2016 +0100

    Merge pull request #113 from nno/_bf/montecarlo_wrong_tail
        BF+BIG+ACK: fix montecarlo_cluster_stat with very weak effects
        that may appear to be significant. Thanks to #Daria Proklova#
        for reporting the issue.

commit ad46d0cc8de08d6cb27c35cce6fd46a836165572
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Nov 27 18:03:42 2016 +0100

    TST: show progress instead of skipping test when on CI platform

 tests/test_montecarlo_cluster_stat_distribution.m | 25 +++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

commit 7139bd0841451d9b6a285cc4a7a0a571617349ee
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Nov 27 17:53:22 2016 +0100

    BF+BIG: fix issue with very weak effects that may appear to be
        significant when using montecarlo_cluster_stat. This bug was
        introduced in commit ee50b05dfea0679e28a8ea5214fe02ae4f937745

 mvpa/cosmo_montecarlo_cluster_stat.m |  4 ++--
 tests/test_montecarlo_cluster_stat.m | 20 ++++++++++----------
 2 files changed, 12 insertions(+), 12 deletions(-)

commit ee50b05dfea0679e28a8ea5214fe02ae4f937745
Merge: 86d55b3 b64fc90
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Nov 25 18:07:20 2016 +0100

    Merge pull request #112 from nno/_bf/monte_carlo_zscore_onetailed
        BF: fix p-value computation that leads to doubling of type-I
        error rate.

commit b64fc909fcf38c1834cfabb1cc896cb5aa53b92a
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 17:43:08 2016 +0100

    TST: clusterize using small dataset

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

commit 49f247c63f8834db4272762e637a7e1a1b69e9e3
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 17:13:44 2016 +0100

    BLD: use 8 threads for coverage

 .travis.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

commit bf1071eb7156adb5b6334c4fbcd425cd495a15e8
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 17:12:25 2016 +0100

    TST: better check to see if we are running CI

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

commit 2fa639d3e4d56710e9d3be90f617bf16eff9b9a6
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 16:27:11 2016 +0100

    BLD+TST: do not test for uniformity when computing coverage on CI
        platform, as this may lead to a stalled build

 tests/test_montecarlo_cluster_stat_distribution.m | 27 ++++++++++++++---------
 1 file changed, 17 insertions(+), 10 deletions(-)

commit 2699a0d864383e4b45e9977d8b8f831dfe54ff26
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 15:30:40 2016 +0100

    BLD+TST: show progress on CI platforms

 tests/test_montecarlo_cluster_stat_distribution.m | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

commit 4e5113ddba00dc91c1004e08dc6d2f026bb8a71d
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Thu Nov 24 14:11:28 2016 +0100

    BF+BIG+BK: fix p-value and z-score computation; previous versions
        returned one-tailed instead of two-tailed z-scored,
        effectively doubling the type-I error rate

 mvpa/cosmo_montecarlo_cluster_stat.m              |  12 ++-
 tests/test_montecarlo_cluster_stat.m              |  73 ++++++++++---
 tests/test_montecarlo_cluster_stat_distribution.m | 124 ++++++++++++++++++++++
 3 files changed, 192 insertions(+), 17 deletions(-)

commit 86d55b37e61321c8d4c3c9fe86391e2727049c15
Merge: b575022 9747343
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Nov 25 14:28:47 2016 +0100

    Merge pull request #111 from nno/_opt/stat_toolbox_check
        OPT: cache presence of stats toolbox

commit b5750222ade185d6c0db2a53dca43423e4102631
Merge: 22eea04 f4e7728
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Fri Nov 25 14:28:34 2016 +0100

    Merge pull request #110 from nno/_opt/isfield          OPT: faster
        check for isfield

commit 97473434692271be92a627d26e45847c3c5730b0
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 13:04:17 2016 +0100

    OPT: cache presence of stats toolbox

 mvpa/cosmo_stat.m | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

commit f4e77289ac92c71f6f2afcfdd4598a56772ac11c
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Fri Nov 25 13:00:40 2016 +0100

    OPT: faster check for isfield

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

commit 22eea047ee79eebe598c295974e645c0cf048b88
Merge: 2f4172a 09e9c42
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Wed Nov 23 17:38:37 2016 +0100

    Merge pull request #109 from
        nno/_nf/ft_support_subj_chan_freq_time          NF: support
        for FieldTrip data with dimord="subj_chan_freq_time"

commit 2f4172af57855fce8a044ddfc063dd1dce2e6f1a
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Nov 23 14:04:39 2016 +0100

    MSL: cosmetic improvements to error message

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

commit 09e9c4283c0cdcef6091993bd8b4aa758d482fb7
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Wed Nov 23 11:10:58 2016 +0100

    NF: support for FieldTrip data with dimord="subj_chan_freq_time"

 mvpa/cosmo_map2meeg.m     | 10 ++++------
 mvpa/cosmo_meeg_dataset.m | 15 +++++++++++++++
 tests/test_meeg_io.m      |  2 ++
 3 files changed, 21 insertions(+), 6 deletions(-)

commit 52a798ad52f9ec3549d9d9bebda223cd9baef6ec
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 17:51:01 2016 +0100

    WEB: fix links

 doc/source/ex_multiple_comparisons.rst | 2 +-
 doc/source/faq.rst                     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit 9cc8a2dd245e18180353fcb3bcef0437045c8fe1
Merge: 1697728 ac10c4e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 15:23:42 2016 +0100

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

commit ac10c4ecd997d04d562203b5b4477065e6f9215c
Merge: f689bf5 0dd6d0a
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Tue Nov 22 15:22:13 2016 +0100

    Merge pull request #108 from nno/rf/parallel_mc_stat          NF:
        parallel montecarlo_cluster_stat

commit 169772858dc73cc9053c1eab8ce98f2634aeaa6e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 15:18:21 2016 +0100

    TST: do not only reset but also switch of warnings

 tests/test_naive_bayes_classifier_searchlight.m | 1 +
 1 file changed, 1 insertion(+)

commit bc55a97b25e28dbecd39683d28014261e6712718
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 15:18:03 2016 +0100

    TST: do not show warnings

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

commit 0dd6d0a68b2c26996ecc09bcddcdfaf53b16f3f7
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 14:31:32 2016 +0100

    ENH: use progress_step to allow for non-integer progress between 0
        and 1

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

commit 8e6bdef55d71901e7049f83f77e5a1b1e4e58da2
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 14:24:29 2016 +0100

    DOC: explain "parallalization" when using single thread in more
        detail

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

commit fbc292452a3b4e95a8e310b5cef45fcb35f3aed2
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 14:24:02 2016 +0100

    RF+DOC: minor simplfications and documentation

 mvpa/cosmo_montecarlo_cluster_stat.m | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

commit bed342e57852f685758de1fada7eac6cf79c0df7
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 14:23:41 2016 +0100

    RF: use cosmo_parcellfun for parallel operations

 mvpa/cosmo_montecarlo_cluster_stat.m | 39 +++++++++++-------------------------
 1 file changed, 12 insertions(+), 27 deletions(-)

commit ce47e857b655b6ea80181a4ee846b989ffd3245a
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 14:15:06 2016 +0100

    RF: use parcellfun for parallel operations

 mvpa/cosmo_searchlight.m | 37 +++++++++----------------------------
 1 file changed, 9 insertions(+), 28 deletions(-)

commit 92e439db9b129a39e13fd36588c4fd60ea71216f
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 14:14:54 2016 +0100

    RF: set center_ids later

 mvpa/cosmo_searchlight.m | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

commit 722ce780306da074e95ae17ab2967476d603b102
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Tue Nov 22 13:47:03 2016 +0100

    NF: general parcellfun for parallel computations

 mvpa/cosmo_parallel_get_nproc_available.m |   2 +-
 mvpa/cosmo_parcellfun.m                   | 129 +++++++++++++++++++++++++
 tests/test_parcellfun.m                   | 150 ++++++++++++++++++++++++++++++
 3 files changed, 280 insertions(+), 1 deletion(-)

commit 597c9092a0401a2b9c5b0a27f9ed8470b89b1bea
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 21 14:05:01 2016 +0100

    MSC: use new syntax for get_nproc_available

 mvpa/cosmo_montecarlo_cluster_stat.m | 4 ++--
 mvpa/cosmo_searchlight.m             | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

commit b91136757970f810adc081b28b9d2142016e0604
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 21 13:34:48 2016 +0100

    RF+DOC+TST: minor refactoring, tests and documentation added

 mvpa/cosmo_parallel_get_nproc_available.m | 85 ++++++++++++++++++++--------
 tests/test_parallel_get_nproc_available.m | 92 +++++++++++++++++++++++++++++++
 2 files changed, 154 insertions(+), 23 deletions(-)

commit 40b4f06c51631d736b6d988b13099ef56ddd42fb
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 21 13:33:53 2016 +0100

    BF: make cosmo_check_external return false for Octave package that
        is available but not loaded

 mvpa/cosmo_check_external.m | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

commit 72b5ca39efee203ef4f5b086e3d9ac0c2209cd24
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Mon Nov 21 11:09:09 2016 +0100

    RF: put progress suffix function back into cluster stat and
        searchlight functions. This means minor code duplication but
        for now it is unclear whether we need the suffix function
        elsewhere

 mvpa/cosmo_montecarlo_cluster_stat.m      | 34 ++++++++++++++++++++-----------
 mvpa/cosmo_parallel_get_progress_suffix.m |  7 -------
 mvpa/cosmo_searchlight.m                  | 14 ++++++++++++-
 3 files changed, 35 insertions(+), 20 deletions(-)

commit f689bf5b4beba2ac26804d31123445a5db0ad072
Merge: 7c9a66f 22d6c0f
Author: Nikolaas N. Oosterhof <n.n.oosterhof@googlemail.com>
Date:   Sun Nov 20 19:09:52 2016 +0100

    Merge pull request #107 from nno/nf/ft_subj_dimord          NF:
        support for FieldTrip data from ft_timelockgrandaverage

commit 22d6c0f47946ee15e3889f7239f305c7397c3e3e
Author: Nikolaas N. Oosterhof <nikolaas.oosterhof@unitn.it>
Date:   Sun Nov 20 17:57:39 2016 +0100

    NF: support for FieldTrip data from ft_timelockgrandaverage

 mvpa/cosmo_map2meeg.m     | 31 +++++++++++++++++++++++--------
 mvpa/cosmo_meeg_dataset.m | 10 ++++++----
 tests/test_meeg_io.m      |  5 +++++
 3 files changed, 34 insertions(+), 12 deletions(-)