LIMO-EEG-Toolbox / limo_tools

Hierarchical Linear Modelling for MEEG data
https://limo-eeg-toolbox.github.io/limo_meeg/
Other
59 stars 27 forks source link

Cluster correction #162

Closed arnodelorme closed 1 year ago

arnodelorme commented 1 year ago

Using Henson Wakeman ERPs

Also, the errors do not help. It would be better if LIMO crashed. Here I cannot fix because it would take me an hour to find where the error is.

Other than that, it works fine.

This is in the master branch. Let’s fix master real quick and release it.

arnodelorme commented 1 year ago

https://github.com/LIMO-EEG-Toolbox/limo_tools/assets/1872705/d2379e00-e4d4-4d8d-8548-6dac323cdc4a

CPernet commented 1 year ago

well it use to work since i used it all winter ... are you sure you path updates haven't messed up stuff

On Thu, 6 Jul 2023 at 11:19, Arnaud Delorme @.***> wrote:

Using Henson Wakeman ERPs

  • One sample t-test cluster correct does not work
  • Two sample t-test cluster correction does not work (ANOVA is fine)

Also, the errors do not help. It would be better if LIMO crashed. Here I cannot fix because it would take me an hour to find where the error is.

Other than that, it works fine.

This is in the master branch. Let’s fix master real quick and release it.

— Reply to this email directly, view it on GitHub https://github.com/LIMO-EEG-Toolbox/limo_tools/issues/162, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABENIDRJXZMHZZPMYG6XMHDXOZ7KXANCNFSM6AAAAAA2AERMJM . You are receiving this because you were assigned.Message ID: @.***>

-- --

-- Dr Cyril Pernet, Neurobiology Research Unit Copenhagen University Hospital, Rigshospitalet Building 8057, Blegdamsvej 9 DK-2100 Copenhagen, Denmark @.***://cpernet.github.io/https://orcid.org/0000-0003-4010-463

CPernet commented 1 year ago

remove your last update of paths and it works

arnodelorme commented 1 year ago

What do you mean by last update of path? Yes, I know how to set up my path, and I am pretty sure it is OK (but could be wrong of course).


/System/Volumes/Data/data/matlab/eeglab
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/realtime/online_eeg
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/realtime/online_meg
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/realtime/online_mri
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/realtime/example
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/contrib/misc
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/contrib/spike
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/test
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/gradiometer
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel/viewprops
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo_tools/deprecated
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo_tools/help
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo_tools/limo_cluster_functions
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo_tools/external/psom
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo_tools/external
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo_tools
    /System/Volumes/Data/data/matlab/eeglab/plugins/get_entropy/functions
    /System/Volumes/Data/data/matlab/eeglab/plugins/get_entropy
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/compat
    /System/Volumes/Data/data/matlab/eeglab/plugins/clean_rawdata/manopt/manopt/solvers/trustregions
    /System/Volumes/Data/data/matlab/eeglab/plugins/clean_rawdata/manopt/manopt/core
    /System/Volumes/Data/data/matlab/eeglab/plugins/clean_rawdata/manopt/manopt/tools
    /System/Volumes/Data/data/matlab/eeglab/plugins/clean_rawdata/manopt/manopt/manifolds/grassmann
    /System/Volumes/Data/data/matlab/eeglab/plugins/clean_rawdata/manopt
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/demofigs
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/arguments
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies/CStrAinBP-2009-09-13
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies/CStrAinBP-2009-09-13/build-Gracing.local
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies/CStrAinBP-2009-09-13/build-Jordan
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies/CStrAinBP-2009-09-13/build-bluffing
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies/CStrAinBP-2009-09-13/build-bluffing-vm
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/dependencies/CStrAinBP-2009-09-13/build-client64-120.sdsc.edu
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/environment
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/helpers
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/keywords
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/bcilab_partial/queries
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/chronux_2_modified
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/chronux_2_modified/spectral_analysis
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/chronux_2_modified/spectral_analysis/continuous
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/chronux_2_modified/spectral_analysis/helper
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/external/shadowplot
    /System/Volumes/Data/data/matlab/eeglab/plugins/Cleanline2.00/utils
    /System/Volumes/Data/data/matlab/eeglab/plugins/BrainBeats/sample_data
    /System/Volumes/Data/data/matlab/eeglab/plugins/BrainBeats/functions
    /System/Volumes/Data/data/matlab/eeglab/plugins/BrainBeats
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo/deprecated
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo/help
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo/limo_cluster_functions
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo/external/psom
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo/external
    /System/Volumes/Data/data/matlab/eeglab/plugins/limo
    /System/Volumes/Data/data/matlab/eeglab/plugins/smi_eyetracking
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect
    /System/Volumes/Data/data/matlab/eeglab/plugins/nsgportal2.1
    /System/Volumes/Data/data/matlab/eeglab/plugins/neuroscanio
    /System/Volumes/Data/data/matlab/eeglab/plugins/musemonitor
    /System/Volumes/Data/data/matlab/eeglab/plugins/mffmatlabio
    /System/Volumes/Data/data/matlab/eeglab/plugins/iirfilt
    /System/Volumes/Data/data/matlab/eeglab/plugins/gazepoint_eyetracking
    /System/Volumes/Data/data/matlab/eeglab/plugins/firfilt
    /System/Volumes/Data/data/matlab/eeglab/plugins/finderscourse1.1
    /System/Volumes/Data/data/matlab/eeglab/plugins/fileio
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip
    /System/Volumes/Data/data/matlab/eeglab/plugins/eegstats
    /System/Volumes/Data/data/matlab/eeglab/plugins/dipfit
    /System/Volumes/Data/data/matlab/eeglab/plugins/data
    /System/Volumes/Data/data/matlab/eeglab/plugins/ctfimport1.04
    /System/Volumes/Data/data/matlab/eeglab/plugins/clean_rawdata
    /System/Volumes/Data/data/matlab/eeglab/plugins/bva-io
    /System/Volumes/Data/data/matlab/eeglab/plugins/brainmovie
    /System/Volumes/Data/data/matlab/eeglab/plugins/bids_dl
    /System/Volumes/Data/data/matlab/eeglab/plugins/bids-matlab-tools
    /System/Volumes/Data/data/matlab/eeglab/plugins/Viewprops1.5.4
    /System/Volumes/Data/data/matlab/eeglab/plugins/SIFT
    /System/Volumes/Data/data/matlab/eeglab/plugins/REST_fieldtrip
    /System/Volumes/Data/data/matlab/eeglab/plugins/PICARD1.0
    /System/Volumes/Data/data/matlab/eeglab/plugins/NihonKoden1.12
    /System/Volumes/Data/data/matlab/eeglab/plugins/MEF3v1.2.2
    /System/Volumes/Data/data/matlab/eeglab/plugins/MARA1.2
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel
    /System/Volumes/Data/data/matlab/eeglab/plugins/FASTER1.2.4
    /System/Volumes/Data/data/matlab/eeglab/plugins/App-MATLABViewer
    /System/Volumes/Data/data/matlab/eeglab/plugins/ANTeepimport1.13
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/connectivity
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/specest
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/inverse
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/preproc
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/trialfun
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/statfun
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/sourcemodel
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/neighbours
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/electrode
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/headmodel
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/anatomy
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/template/layout
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/external/fileexchange
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/brainstorm
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/ssgc_v1.0
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/nolte
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/mvgc_v1.0/utils/control
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/mvgc_v1.0/utils
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/mvgc_v1.0/stats
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/mvgc_v1.0/core
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/mvgc_v1.0
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/haufe
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/export_fig
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/libs/Daniele_ARMA
    /System/Volumes/Data/data/matlab/eeglab/plugins/roiconnect/newscripts
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/plotting
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/utilities
    /System/Volumes/Data/data/matlab/eeglab/plugins/fieldtrip/forward
    /System/Volumes/Data/data/matlab/eeglab/plugins/eegstats/restingIAF
    /System/Volumes/Data/data/matlab/eeglab/plugins/brainmovie/x3d_version3g
    /System/Volumes/Data/data/matlab/eeglab/plugins/biosig/biosig/doc
    /System/Volumes/Data/data/matlab/eeglab/plugins/biosig/biosig/t250_ArtifactPreProcessingQualityControl
    /System/Volumes/Data/data/matlab/eeglab/plugins/biosig/biosig/t200_FileAccess
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel/matconvnet/examples
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel/matconvnet/matlab/xtest
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel/matconvnet/matlab/simplenn
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel/matconvnet/matlab/mex
    /System/Volumes/Data/data/matlab/eeglab/plugins/ICLabel/matconvnet/matlab
    /System/Volumes/Data/data/matlab/eeglab/plugins
    /System/Volumes/Data/data/matlab/eeglab/functions/supportfiles
    /System/Volumes/Data/data/matlab/eeglab/functions/miscfunc
    /System/Volumes/Data/data/matlab/eeglab/functions/timefreqfunc
    /System/Volumes/Data/data/matlab/eeglab/functions/statistics
    /System/Volumes/Data/data/matlab/eeglab/functions/popfunc
    /System/Volumes/Data/data/matlab/eeglab/functions/studyfunc
    /System/Volumes/Data/data/matlab/eeglab/functions/guifunc
    /System/Volumes/Data/data/matlab/eeglab/functions/sigprocfunc
    /System/Volumes/Data/data/matlab/eeglab/functions
    /System/Volumes/Data/data/matlab/eeglab/functions/adminfunc
CPernet commented 1 year ago

the error is NOT an error, it is that it is not significant but because you turned that info off you GUI bugs - I think it is fixed now via a series of small changes, can you try?

CPernet commented 1 year ago

solved -- not a cluster problem, the bootstrap computed was incorrect

arnodelorme commented 1 year ago

Cool