lock files

README.md

@@ -2,74 +2,72 @@
 
 # **EEG Preprocessing**
 
-Steps 1-4 create filters (e.g., from the ICA, segment labeling), which later get applied to the raw data starting in step 5.
+Steps 1-4 create preprocessing information (e.g., from the ICA, segment labeling), that later is applied to the raw data starting in step 5.
 
 All steps use FieldTrip and were executed within MATLAB 2020a.
 
 Deviations from the standard pipeline:
 
-- no ECG available, which would normally guide heart component labeling
-- all scripts have been adapted to single run
+- no ECG was available, which would normally guide heart IC labeling
+- all scripts have been adapted to work on a single run
+
+Many scripts were run on the high performance computing cluster (HPC) at the Max Planck Institute for Human Development (Berlin, Germany). One of two different deployment approaches was used: either (a) the relevant script was compiled or (b) the script was directly called with multiple MATLAB instances. In the case of (a), the respective code folder will contain a "_prepare" file that was used to compile the code, as well as a '_START' bash script, that deployed the compiled code; in the case of (b) bo compiling was done, and the '_START' script immediately calls the relevant MATLAB code. To re-run scripts outside of the HPC environment,
+a script needs to be written that loops the script across all subjects. Note that for debugging purposes, code usually checks whether it is run on a mac, and if so, performs all computations on an example subject. Depending on the deployment situation, this section may need to be adapted.
 
 ---
 
-### **01_prepare_preprocessing**
+### **a1_prepare_preprocessing**
 
 - Prepare for ICA
 - Read into FieldTrip format
-- Switch channels
-- EEG settings:
-  - Referenced to avg. mastoid (A1, A2)
-  - downsample: 1000Hz to 250 Hz
-  - 4th order Butterworth 1-100 Hz BPF
-  - no reref for ECG
+- Referenced to avg. mastoid (A1, A2)
+- downsample: 1000Hz to 250 Hz
+- 4th order Butterworth 1-100 Hz BPF
 
-### **02_visual_inspection**
+### **a2_visual_inspection**
 
-- Check for gross noise periods that should not be considered for ICA
+- Manual labeling of noise periods that will be excluded prior to ICA
 
-### **03_ica**
+### **a3_ica**
 
-- Conduct initial ICA1, this should be run on tardis
+- prior to ICA, data are segmented into 2 s pseudo-trials
+- ICA is conducted
+- use VEOG, HEOG and ECG (not available) to pre-label blink, eye move and heart ICs
 
-### **04_ica_labeling**
+### **a4_ica_labeling**
 
 - Manual labeling of artefactual ICA components
 
-### **05_segmentation_raw_data**
+### **a5_segmentation_raw_data**
 
-- Segmentation: -1500 ms relative to fixcue onset to 1500 ms after ITI onset
-- Load raw data
-- Switch channels
+This step loads the raw data again and segments them to the desired time window, prior filters will be applied to these data in the next step.
+
+- load raw data
+- segment to -1s to +2s relative to stimulus onset
 - EEG settings:
   - Referenced to avg. mastoid (A1, A2)
+  - recover implicit reference: POz
   - 0.2 4th order butterworth HPF
   - 125 4th order butterworth LPF
   - demean
-  - recover implicit reference: POz
-  - downsample: 1000Hz to 500 Hz
+  - downsample: 512 Hz to 500 Hz
+
+### **a6_automatic_artifact_correction**
 
-### **06_automatic_artifact_correction**
+Identify additional artifacts after removing ICA components. This step does NOT yet remove anything. We only calculate the data to be removed in the next step.
 
-- Automatic artifact correction, interpolation
-- Remove blink, move, heart, ref, art & emg ICA components prior to calculation
 - get artifact contaminated channels by kurtosis, low & high frequency artifacts
 - get artifact contaminated channels by FASTER
 - interpolate artifact contaminated channels
 - get artifact contaminated epochs & exclude epochs recursively
 - get channel x epoch artifacts
-- Note that this does NOT yet remove anything. We only calculate the data to be removed in the next step.
 
-### **07_prep_data_for_analysis**
+### **a7_prep_data_for_analysis**
 
 - Remove blink, move, heart, ref, art & emg ICA components
-- Interpolate detected artifact channels
-- Remove artifact-heavy trials, for subjects with missing onsets, the missing trials are included here as "artefactual trials", hence correcting the EEG-behavior assignment:
-
-### **08_assignConditionsToData**
-
-- Remove additional channels
-- Load behavioral data and add information to data
+- Remove artifact-heavy trials
+- Interpolate artifact-heavy channels
+- output: preprocessed data: 'sub-XXX_task-xxxx_eeg_art.mat'
 
 ---
 

code/.gitattributes

@@ -1 +0,0 @@
-* annex.largefiles=nothing

code/a4_ica_labeling.m

@@ -1,89 +0,0 @@
-%% a4_ica_labeling
-
-% required functions:
-% - cm_label_ica_gui_20180116
-
-currentFile = mfilename('fullpath');
-[pathstr,~,~] = fileparts(currentFile);
-cd(fullfile(pathstr,'..'))
-rootpath = pwd;
-
-% inputs
-pn.eeg_BIDS = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'eeg_BIDS');
-pn.channel_locations = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'channel_locations');
-pn.events = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'events');
-pn.tools = fullfile(rootpath, 'tools');
-% outputs
-pn.eeg_ft = fullfile(rootpath, 'data', 'outputs', 'eeg');
-pn.history = fullfile(rootpath, 'data', 'outputs', 'history');
-
-addpath(fullfile(pn.tools, 'fieldtrip')); ft_defaults;
-addpath(fullfile(pn.tools, 'helpers'));
-
-%% define IDs for visual screening
-
-ID = 'sub-002';
-
-%% load data & start GUI
-
-% load data (full data)
-load(fullfile(pn.eeg_ft, [ID, '_task-xxxx_eeg_ica.mat']),'data');
-
-if ~isfield(data.iclabels,'emg')
-    data.iclabels.emg = [];
-end
-
-% load config (ICA version)
-load(fullfile(pn.history, [ID, '_task-xxxx_config.mat']),'config');
-
-% settings for ICA
-
-% ica config
-cfg.method           = config.ica1.cfg.method; %'runica';
-cfg.trials           = 'all';
-cfg.numcomponent     = 'all';
-cfg.demean           = 'no';
-cfg.runica.extended  = 1;
-
-% ICA solution for segments
-cfg.unmixing     = data.unmixing;
-cfg.topolabel    = data.topolabel;
-
-% ICA (from weights)
-
-% components
-comp = ft_componentanalysis(cfg,data);
-    
-% include electrode information
-comp.elec = data.elec;
-
-% include ICA labeling
-comp.iclabels = data.iclabels;
-
-% clear cfg
-clear cfg
-
-% label ICs
-
-% settings
-cfg.topoall  = 'yes';
-cfg.chanlocs = data.chanlocs;
-
-% label electrodes
-data.iclabels = cm_label_ica_gui_20180116(cfg,comp);
-
-% keep labels in config
-config.ica1.iclabels.manual = data.iclabels;
-
-% clear variables
-clear cfg
-
-% save data (full data)
-save(fullfile(pn.eeg_ft, [ID, '_task-xxxx_eeg_ica.mat']),'data');
-
-% save config (ICA version)
-save(fullfile(pn.history, [ID, '_task-xxxx_config.mat']),'config');
-
-% clear variables
-
-clear BLOCK ID comp config data

code/a4_ica_labeling.m

@@ -0,0 +1 @@
+../.git/annex/objects/pK/2f/MD5E-s2138--2f6104c96200fceee2997f1b2b163cef.m/MD5E-s2138--2f6104c96200fceee2997f1b2b163cef.m

code/a5_segmentation_raw_data/a5_segmentation_raw_data.m

@@ -1,135 +0,0 @@
-function a5_segmentation_raw_data(id, rootpath)
-
-if ismac % run if function is not pre-compiled
-    id = '1'; % test for example subject
-    currentFile = mfilename('fullpath');
-    [pathstr,~,~] = fileparts(currentFile);
-    cd(fullfile(pathstr,'..', '..'))
-    rootpath = pwd;
-end
-
-% inputs
-pn.eeg_BIDS = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'eeg_BIDS');
-pn.channel_locations = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'channel_locations');
-pn.events = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'events');
-pn.tools = fullfile(rootpath, 'tools');
-% outputs
-pn.eeg_ft = fullfile(rootpath, 'data', 'outputs', 'eeg');
-pn.history = fullfile(rootpath, 'data', 'outputs', 'history');
-
-if ismac % run if function is not pre-compiled
-     addpath(fullfile(pn.tools, 'fieldtrip')); ft_defaults;
-     addpath(fullfile(pn.tools, 'helpers'));
-end
-
-% N = 33
-IDs = tdfread(fullfile(pn.eeg_BIDS, 'participants.tsv'));
-IDs = cellstr(IDs.participant_id);
-
-id = str2num(id);
-
-display(['processing ID ' num2str(IDs{id})]);
-    
-%%  load raw data
-
-if ~exist(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_seg.mat']),'file')
-
-    % load config
-    config = [];
-    load(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
-
-    %% load events file
-    
-    events = readtable(fullfile(pn.events, ['EMP',IDs{id}(end-1:end),'_events.csv']));
-    
-    %% generate segmentation structure
-
-    % load marker file
-    mrk = config.mrk;
-    
-    % generate trial structure
-    mrk_val = {mrk(1,:).value};
-    indOnset = find(strcmp(mrk_val(:),'boundary')) + 1;
-    mrk_val = mrk_val(indOnset:end);
-
-    % Stim trials
-    fsample = 512;
-    trl = zeros(length(mrk_val),3);
-    TOI1 = 1*fsample; % segmentation before trigger (in 1024 Hz)
-    TOI2 = 2*fsample; % segmentation following trigger
-
-    for j = 1:size(trl,1)
-        trl(j,1) = mrk(1,indOnset+j-1).sample - TOI1;
-        trl(j,2) = mrk(1,indOnset+j-1).sample + TOI2;
-        trl(j,3) = -TOI1; % offset
-    end; clear j
-
-    % add trial structure to config
-    config.trl = trl;
-
-    %% load, filter, and re-reference raw data
-
-    % define reading & preprocessing parameters
-    % read in all data first
-
-    % load data
-    cfg           = [];
-    cfg.datafile  = ...
-        fullfile(pn.eeg_BIDS, IDs{id}, 'eeg', [IDs{id}, '_task-xxxx_eeg.eeg']);
-    cfg.trl         = config.trl;
-    cfg.channel     = {'all'};
-
-    data_eeg            = ft_preprocessing(cfg);
-
-    %% reref & filter EEG data
-    
-    cfg             = [];
-
-    cfg.continuous  = 'yes';
-    cfg.demean      = 'yes';
-
-    cfg.reref       = 'yes';
-    cfg.refmethod   = 'avg';
-    cfg.refchannel  = {'M1', 'M2'};
-    cfg.implicitref = 'POz';
-
-    cfg.hpfilter    = 'yes';
-    cfg.hpfreq      = .2;
-    cfg.hpfiltord   = 4;
-    cfg.hpfilttype  = 'but';
-
-    cfg.lpfilter    = 'yes';
-    cfg.lpfreq      = 125;
-    cfg.lpfiltord   = 4;
-    cfg.lpfilttype  = 'but';
-
-    % get data
-    data_eeg = ft_preprocessing(cfg, data_eeg);
-    flt = cfg;
-
-    % clear cfg structure
-    clear cfg
-
-    %% resample to 500 Hz
-
-    % define settings for resampling
-    cfg.resamplefs = 500;
-    cfg.detrend    = 'no';
-    cfg.feedback   = 'no';
-    cfg.trials     = 'all';
-    data_eeg    = ft_resampledata(cfg,data_eeg);
-
-    resample = cfg;
-    % clear variables
-    clear cfg
-
-    % update config
-    config.seg.flt = flt;
-    config.seg.resample = resample;
-
-    %% save eeg data and history
-    
-    save(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_seg.mat']),'data_eeg', 'events');
-    save(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
-
-end % exist

code/a5_segmentation_raw_data/a5_segmentation_raw_data.m

@@ -0,0 +1 @@
+../../.git/annex/objects/g3/XK/MD5E-s3752--6a4119f7e05769d6907083f356fddd7c.m/MD5E-s3752--6a4119f7e05769d6907083f356fddd7c.m

code/a5_segmentation_raw_data/logs/eegmp_prep_33.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/p8/Z2/MD5E-s265--b47bd2cd9de9755d7419721772ae9a20.out/MD5E-s265--b47bd2cd9de9755d7419721772ae9a20.out

code/a6_automatic_artifact_correction/a6_automatic_artifact_correction.m

@@ -1,249 +0,0 @@
-function a6_automatic_artifact_correction(id, rootpath)
-
-if ismac % run if function is not pre-compiled
-    id = '1'; % test for example subject
-    currentFile = mfilename('fullpath');
-    [pathstr,~,~] = fileparts(currentFile);
-    cd(fullfile(pathstr,'..', '..'))
-    rootpath = pwd;
-end
-
-% inputs
-pn.eeg_BIDS = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'eeg_BIDS');
-pn.channel_locations = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'channel_locations');
-pn.events = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'events');
-pn.tools = fullfile(rootpath, 'tools');
-% outputs
-pn.eeg_ft = fullfile(rootpath, 'data', 'outputs', 'eeg');
-pn.history = fullfile(rootpath, 'data', 'outputs', 'history');
-
-if ismac % run if function is not pre-compiled
-     addpath(fullfile(pn.tools, 'fieldtrip')); ft_defaults;
-     addpath(fullfile(pn.tools, 'helpers'));
-end
-
-% N = 33
-IDs = tdfread(fullfile(pn.eeg_BIDS, 'participants.tsv'));
-IDs = cellstr(IDs.participant_id);
-
-id = str2num(id);
-
-display(['processing ID ' num2str(IDs{id})]);
-
-%% load data
-
-load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_seg.mat']),'data_eeg', 'events');
-
-% remove M2 (collinear with M1 due to avg. mastoid REF: mean(M1,M2)=0)
-cfg_preproc               = [];
-cfg_preproc.channel       = {'all', '-M2'};
-data_eeg = ft_preprocessing(cfg_preproc, data_eeg);
-
-data_ica = load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_ica.mat']),'data');
-
-data = data_eeg; clear data_eeg;
-data.elec = data_ica.data.elec;
-data.chanlocs = data_ica.data.chanlocs; clear data_ica;
-
-%% ------------------ ARTIFACT DETECTION - PREPARATION ----------------- %%
-
-% load config
-
-load(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
-
-config.elec = data.elec;
-
-%% ICA (from weights)
-
-% ica config
-cfg.method           = 'runica';
-cfg.channel          = {'all'}; % additional channels should be excluded already...
-cfg.trials           = 'all';
-cfg.numcomponent     = 'all';
-cfg.demean           = 'yes';
-cfg.runica.extended  = 1;
-
-% ICA solution
-cfg.unmixing     = config.ica1.unmixing;
-cfg.topolabel    = config.ica1.topolabel;
-
-% components
-comp = ft_componentanalysis(cfg,data);
-
-% clear cfg
-clear cfg data
-
-%% remove components
-
-% get IC labels
-iclabels = config.ica1.iclabels.manual;
-
-% cfg for rejecting components (reject: blinks, eye movements,
-% ecg, ref); JQK: added artifacts and emg
-cfg.component = sortrows([iclabels.bli(:); iclabels.mov(:); iclabels.hrt(:); iclabels.ref(:); iclabels.art(:); iclabels.emg(:)])';
-cfg.demean    = 'yes';
-
-% reject components
-data = ft_rejectcomponent(cfg,comp);
-
-% clear cfg
-clear cfg comp
-
-%% remove eye & reference channels
-
-cfg.channel     = {'all','-IO1','-IO2','-M1','-VEOG','-HEOG'};
-cfg.demean      = 'yes';
-
-% remove channels
-tmpdat = ft_preprocessing(cfg,data);
-
-% clear cfg & data variable
-clear cfg data
-
-%% ------------------------- ARTIFACT DETECTION ------------------------ %%
-
-% open log file
-fid = fopen(fullfile(pn.history, [IDs{id}, '_task-xxxx_ArtCorr.txt']),'a');
-
-fprintf(fid,['*********************   BLOCK   *********************\n']);
-fprintf(fid,['function: a6_automatic_artifact_correction.m \n\n']);                
-fprintf(fid,['eeg file = ' config.data_file '\n\n']);
-
-n_trl = length(tmpdat.trial);
-
-%%  get artifact contaminated channels by kurtosis, low & high frequency artifacts
-
-cfg.criterion = 3;
-cfg.recursive = 'no';
-
-[index0 parm0 zval0] = cm_MWB_channel_x_epoch_artifacts_20170922(cfg,tmpdat);
-
-% write log
-tmp_log = '';
-for j = 1:length(index0.c)
-    tmp_log = [tmp_log num2str(index0.c(j)) ' '];
-end; clear j
-tmp_log = [tmp_log(1:end-1) '\n'];
-fprintf(fid,'(1) automatic bad channel detection:\n');
-fprintf(fid,['MWB:          channel(s) ' tmp_log]);
-
-% clear cfg
-clear cfg tmp_log
-
-%%  get artifact contaminated channels by FASTER
-
-cfg.criterion = 3;
-cfg.recursive = 'no';
-
-[index1 parm1 zval1] = THG_FASTER_1_channel_artifacts_20140302(cfg,tmpdat);
-
-% write log
-tmp_log = '';
-for j = 1:length(index1)
-    tmp_log = [tmp_log num2str(index1(j)) ' '];
-end; clear j
-tmp_log = [tmp_log(1:end-1) '\n'];
-fprintf(fid,['FASTER:      channel(s) ' tmp_log]);
-
-% clear cfg
-clear cfg tmp_log
-
-%%  interpolate artifact contaminated channels
-
-% collect bad channels
-badchan = unique([index0.c; index1]);
-
-fprintf(fid,['--> ' num2str(length(badchan)) ' channels interpolated\n\n']);
-
-cfg.method     = 'spline';
-cfg.badchannel = tmpdat.label(badchan);
-cfg.trials     = 'all';
-cfg.lambda     = 1e-5; 
-cfg.order      = 4; 
-cfg.elec       = config.elec;
-
-% interpolate
-tmpdat = ft_channelrepair(cfg,tmpdat);
-
-% clear cfg
-clear cfg
-
-%% equalize duration of trials to the trial with fewest samples
-
-for indTrial = 1:numel(tmpdat.trial)
-    TrialLength(indTrial) = size(tmpdat.trial{indTrial},2);
-end
-[val, idx] = min(TrialLength);
-for indTrial = 1:numel(tmpdat.trial)
-    tmpdat.trial{indTrial} = tmpdat.trial{indTrial}(:,1:val);
-    tmpdat.time{indTrial} = tmpdat.time{idx};
-end
-
-%%  get artifact contaminated epochs & exclude epochs
-% includes: - THG_MWB_channel_x_epoch_artifacts_20140311
-%           - THG_FASTER_2_epoch_artifacts_20140302
-% recursive epoch exclusion!
-
-[tmpdat index] = THG_automatic_artifact_correction_trials_20170922(tmpdat);
-
-% write log
-fprintf(fid,'(2) automatic recursive bad epoch detection:\n');
-fprintf(fid,['MWB & FASTER: ' num2str(n_trl-length(index)) ' bad epoch(s) detected\n\n']);
-
-%%  get channel x epoch artifacts
-
-% cfg
-cfg.criterion = 3;
-cfg.recursive = 'yes';
-
-[index3 parm3 zval3] = THG_FASTER_4_channel_x_epoch_artifacts_20140302(cfg,tmpdat);
-
-% write log
-fprintf(fid,'(3) automatic single epoch/channel detection:\n');
-fprintf(fid,['FASTER:       ' num2str(sum(sum(index3))) ' channel(s) x trial(s) detected\n\n']);
-
-% clear cfg
-clear cfg
-
-%%  collect and save detected artifacts & artifact correction infos
-
-% include ArtDect.parameters
-
-% bad channels
-ArtDect.channels = badchan;
-
-% bad trials
-tmp  = zeros(n_trl,1); tmp(index,1) = 1;
-badtrl = find(tmp==0);
-ArtDect.trials  = badtrl; 
-clear tmp
-
-% bad single epoch(s)/channel(s) - after exclusion of bad epochs
-ArtDect.channels_x_trials = index3;
-
-% overview
-ind = [1:n_trl];
-ind(badtrl) = [];
-tmp = ones(length(tmpdat.label),n_trl);
-tmp(:,ind) = index3;
-tmp(badchan,:) = 1;
-ArtDect.channels_x_trials_all = tmp;
-clear tmp
-
-% save version
-ArtDect.version = 'JQK 20180123';
-
-% add to config
-config.ArtDect = ArtDect;
-
-% save config
-save(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
-
-%%  finalize log
-
-% log
-fprintf(fid,'Artifact detection completed.\n');
-fprintf(fid,['Information saved to: ' IDs{id} '_config.mat\n\n']);
-fclose(fid);
-
-end

code/a6_automatic_artifact_correction/a6_automatic_artifact_correction.m

@@ -0,0 +1 @@
+../../.git/annex/objects/kM/7V/MD5E-s6925--6213a2869ce3496f9aa1a025de3c687d.m/MD5E-s6925--6213a2869ce3496f9aa1a025de3c687d.m

code/a6_automatic_artifact_correction/logs/eegmp_art_1.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/7K/Kq/MD5E-s7727--e535074c317e819248b92d21151cc325.out/MD5E-s7727--e535074c317e819248b92d21151cc325.out

code/a6_automatic_artifact_correction/logs/eegmp_art_10.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/FX/KX/MD5E-s7858--d79988157f1bbe98ce4cd7d326a4b01f.out/MD5E-s7858--d79988157f1bbe98ce4cd7d326a4b01f.out

code/a6_automatic_artifact_correction/logs/eegmp_art_11.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/7z/PX/MD5E-s7914--129d04a988b288fc5cb1abb9605b8d03.out/MD5E-s7914--129d04a988b288fc5cb1abb9605b8d03.out

code/a6_automatic_artifact_correction/logs/eegmp_art_12.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/25/w1/MD5E-s7724--3e6118250c6fae55657c1db4e10c0c4a.out/MD5E-s7724--3e6118250c6fae55657c1db4e10c0c4a.out

code/a6_automatic_artifact_correction/logs/eegmp_art_13.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/Q8/k8/MD5E-s7664--499199cdea082a17c1704da497568265.out/MD5E-s7664--499199cdea082a17c1704da497568265.out

code/a6_automatic_artifact_correction/logs/eegmp_art_14.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/0K/07/MD5E-s7864--52cd9c233495ddbc6ddfaef0d06395d5.out/MD5E-s7864--52cd9c233495ddbc6ddfaef0d06395d5.out

code/a6_automatic_artifact_correction/logs/eegmp_art_15.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/zx/PV/MD5E-s7794--01f42be5c7eb49b63d2abe69ed9cd024.out/MD5E-s7794--01f42be5c7eb49b63d2abe69ed9cd024.out

code/a6_automatic_artifact_correction/logs/eegmp_art_16.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/3w/0f/MD5E-s7660--e31814501e1ac2f2c40e6a15cffcf78e.out/MD5E-s7660--e31814501e1ac2f2c40e6a15cffcf78e.out

code/a6_automatic_artifact_correction/logs/eegmp_art_17.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/PJ/zq/MD5E-s7860--c1ae41d3b3622de282cd60b00bfcdeb9.out/MD5E-s7860--c1ae41d3b3622de282cd60b00bfcdeb9.out

code/a6_automatic_artifact_correction/logs/eegmp_art_18.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/5K/1W/MD5E-s7657--403238dc66cbe674e3b1ed0f80759669.out/MD5E-s7657--403238dc66cbe674e3b1ed0f80759669.out

code/a6_automatic_artifact_correction/logs/eegmp_art_19.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/gX/F6/MD5E-s7662--f3f4a2de8e42167bc285b17ef09b94bf.out/MD5E-s7662--f3f4a2de8e42167bc285b17ef09b94bf.out

code/a6_automatic_artifact_correction/logs/eegmp_art_2.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/1k/g4/MD5E-s7794--e79ac87bd19271c2542d4d7d352237f9.out/MD5E-s7794--e79ac87bd19271c2542d4d7d352237f9.out

code/a6_automatic_artifact_correction/logs/eegmp_art_20.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/QP/MF/MD5E-s7788--17d71d6b78b745aa8901c68df8b706bc.out/MD5E-s7788--17d71d6b78b745aa8901c68df8b706bc.out

code/a6_automatic_artifact_correction/logs/eegmp_art_21.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/wg/gp/MD5E-s151221--18d61b069a95763add6e515b9424e884.out/MD5E-s151221--18d61b069a95763add6e515b9424e884.out

code/a6_automatic_artifact_correction/logs/eegmp_art_22.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/w9/6q/MD5E-s7529--b02d5f46b58351957356a2b42774864f.out/MD5E-s7529--b02d5f46b58351957356a2b42774864f.out

code/a6_automatic_artifact_correction/logs/eegmp_art_23.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/Jj/mW/MD5E-s7792--2c562638d0694951a296f6ceb77e79c4.out/MD5E-s7792--2c562638d0694951a296f6ceb77e79c4.out

code/a6_automatic_artifact_correction/logs/eegmp_art_24.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/zW/Q5/MD5E-s7727--2d8aedad3f750e83c509304bcd069b47.out/MD5E-s7727--2d8aedad3f750e83c509304bcd069b47.out

code/a6_automatic_artifact_correction/logs/eegmp_art_25.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/f9/8k/MD5E-s7527--008796c9176aa810f2ac4326f3892e82.out/MD5E-s7527--008796c9176aa810f2ac4326f3892e82.out

code/a6_automatic_artifact_correction/logs/eegmp_art_26.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/gF/1Z/MD5E-s7726--fd23775c67b067f25b2e736f6169772c.out/MD5E-s7726--fd23775c67b067f25b2e736f6169772c.out

code/a6_automatic_artifact_correction/logs/eegmp_art_27.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/vJ/xv/MD5E-s7666--85322bc3bd344aa5d21fb3af0dff5317.out/MD5E-s7666--85322bc3bd344aa5d21fb3af0dff5317.out

code/a6_automatic_artifact_correction/logs/eegmp_art_28.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/WV/Z5/MD5E-s7665--445f926ae88a37360ee6ac1045828f3d.out/MD5E-s7665--445f926ae88a37360ee6ac1045828f3d.out

code/a6_automatic_artifact_correction/logs/eegmp_art_29.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/gJ/Kf/MD5E-s7596--e859b3e3144473c4c36316e4b8260dc2.out/MD5E-s7596--e859b3e3144473c4c36316e4b8260dc2.out

code/a6_automatic_artifact_correction/logs/eegmp_art_3.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/p9/Q7/MD5E-s7857--07f05d5b69ab94dc8a1945234360712c.out/MD5E-s7857--07f05d5b69ab94dc8a1945234360712c.out

code/a6_automatic_artifact_correction/logs/eegmp_art_30.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/vQ/G3/MD5E-s7594--f2a4fa8b2841d4600498ceba758dcd9c.out/MD5E-s7594--f2a4fa8b2841d4600498ceba758dcd9c.out

code/a6_automatic_artifact_correction/logs/eegmp_art_31.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/wz/55/MD5E-s6741--1fa4eb52ecbc1c8c88368255ed8fb326.out/MD5E-s6741--1fa4eb52ecbc1c8c88368255ed8fb326.out

code/a6_automatic_artifact_correction/logs/eegmp_art_32.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/qg/6X/MD5E-s6681--bc2af5c9918a742136adf43f0f218747.out/MD5E-s6681--bc2af5c9918a742136adf43f0f218747.out

code/a6_automatic_artifact_correction/logs/eegmp_art_33.out

@@ -1,96 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-033
-Warning: sampleinfo in the configuration is inconsistent with the actual data
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a6_aut0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/fixsampleinfo.m' at line 100
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a6_aut0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 148
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a6_aut0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a6_aut0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_preprocessing.m' at line 288
-
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 991 MB
-preprocessing
-preprocessing trial 6 from 1200preprocessing trial 141 from 1200preprocessing trial 291 from 1200preprocessing trial 438 from 1200preprocessing trial 589 from 1200preprocessing trial 740 from 1200preprocessing trial 892 from 1200preprocessing trial 1040 from 1200preprocessing trial 1185 from 1200preprocessing trial 1200 from 1200
-the call to "ft_preprocessing" took 3 seconds and required the additional allocation of an estimated 1013 MB
-the input is raw data with 71 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-           hdr: [1x1 struct]
-       fsample: 500
-    sampleinfo: [1200x2 double]
-         trial: {1x1200 cell}
-          time: {1x1200 cell}
-         label: {71x1 cell}
-           cfg: [1x1 struct]
-          elec: [1x1 struct]
-      chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-           hdr: [1x1 struct]
-       fsample: 500
-    sampleinfo: [1200x2 double]
-         trial: {1x1200 cell}
-          time: {1x1200 cell}
-         label: {71x1 cell}
-           cfg: [1x1 struct]
-          elec: [1x1 struct]
-      chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-           hdr: [1x1 struct]
-       fsample: 500
-    sampleinfo: [1200x2 double]
-         trial: {1x1200 cell}
-          time: {1x1200 cell}
-         label: {71x1 cell}
-           cfg: [1x1 struct]
-          elec: [1x1 struct]
-      chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-           hdr: [1x1 struct]
-       fsample: 500
-    sampleinfo: [1200x2 double]
-         trial: {1x1200 cell}
-          time: {1x1200 cell}
-         label: {71x1 cell}
-           cfg: [1x1 struct]
-          elec: [1x1 struct]
-      chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-           hdr: [1x1 struct]
-       fsample: 500
-    sampleinfo: [1200x2 double]
-         trial: {1x1200 cell}
-          time: {1x1200 cell}
-         label: {71x1 cell}
-           cfg: [1x1 struct]
-          elec: [1x1 struct]
-      chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-baseline correcting data 
-scaling data with 1 over 105.766780
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 4 seconds and required the additional allocation of an estimated 1006 MB
-Reference to non-existent field 'manual'.
-
-Error in a6_automatic_artifact_correction (line 79)
-
-MATLAB:nonExistentField

code/a6_automatic_artifact_correction/logs/eegmp_art_33.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/XQ/wV/MD5E-s998593--f6878c4db0394b8ba2df6a56abfda8a9.out/MD5E-s998593--f6878c4db0394b8ba2df6a56abfda8a9.out

code/a6_automatic_artifact_correction/logs/eegmp_art_4.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/8Q/3f/MD5E-s7659--a5b073124b66f9b590540b4decaf2a3f.out/MD5E-s7659--a5b073124b66f9b590540b4decaf2a3f.out

code/a6_automatic_artifact_correction/logs/eegmp_art_5.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/mv/2X/MD5E-s7664--b986c08c7ae0837ae4881a8c118bbf5e.out/MD5E-s7664--b986c08c7ae0837ae4881a8c118bbf5e.out

code/a6_automatic_artifact_correction/logs/eegmp_art_6.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/FJ/45/MD5E-s7659--820ab320b98744946c7b679fb561d69c.out/MD5E-s7659--820ab320b98744946c7b679fb561d69c.out

code/a6_automatic_artifact_correction/logs/eegmp_art_7.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/mQ/FZ/MD5E-s7727--fe28f5e93153a5172ec7f3497b22f355.out/MD5E-s7727--fe28f5e93153a5172ec7f3497b22f355.out

code/a6_automatic_artifact_correction/logs/eegmp_art_8.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/wG/Vf/MD5E-s7859--ebb0925c9a47c7127dc787fec1de7132.out/MD5E-s7859--ebb0925c9a47c7127dc787fec1de7132.out

code/a6_automatic_artifact_correction/logs/eegmp_art_9.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/qG/kv/MD5E-s7659--0e1e450228313f14a703c11c18d3118e.out/MD5E-s7659--0e1e450228313f14a703c11c18d3118e.out

code/a7_prep_data_for_analysis/a7_prep_data_for_analysis

@@ -0,0 +1 @@
+../../.git/annex/objects/81/V7/MD5E-s48778671--437acfef9e372e09c35ebfe66240b5b7/MD5E-s48778671--437acfef9e372e09c35ebfe66240b5b7

code/a7_prep_data_for_analysis/a7_prep_data_for_analysis.m

@@ -1,171 +0,0 @@
-function a7_prep_data_for_analysis(id, rootpath)
-
-if ismac % run if function is not pre-compiled
-    id = '1'; % test for example subject
-    currentFile = mfilename('fullpath');
-    [pathstr,~,~] = fileparts(currentFile);
-    cd(fullfile(pathstr,'..', '..'))
-    rootpath = pwd;
-end
-
-% inputs
-pn.eeg_BIDS = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'eeg_BIDS');
-pn.channel_locations = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'channel_locations');
-pn.events = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'events');
-pn.tools = fullfile(rootpath, 'tools');
-% outputs
-pn.eeg_ft = fullfile(rootpath, 'data', 'outputs', 'eeg');
-pn.history = fullfile(rootpath, 'data', 'outputs', 'history');
-
-if ismac % run if function is not pre-compiled
-     addpath(fullfile(pn.tools, 'fieldtrip')); ft_defaults;
-     addpath(fullfile(pn.tools, 'helpers'));
-end
-
-% N = 33
-IDs = tdfread(fullfile(pn.eeg_BIDS, 'participants.tsv'));
-IDs = cellstr(IDs.participant_id);
-
-id = str2num(id);
-
-display(['processing ID ' num2str(IDs{id})]);
-
-%% load files
-
-% load data
-load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_seg.mat']),'data_eeg', 'events');
-
-data_ica = load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_ica.mat']),'data');
-data = data_eeg; clear data_eeg;
-data.elec = data_ica.data.elec;
-data.chanlocs = data_ica.data.chanlocs; clear data_ica;
-
-% load config
-load(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
-
-%% define parameter
-
-% ICs to reject
-iclabels    = config.ica1.iclabels.manual;
-ics2reject = [iclabels.bli(:); iclabels.mov(:); iclabels.hrt(:); iclabels.ref(:); iclabels.art(:); iclabels.emg(:)];
-clear iclabels
-
-% trials to remove
-trls2remove = config.ArtDect.trials;
-
-% channels to interpolate
-chns2interp = config.ArtDect.channels;
-
-%% ICA (from weights)
-
-% ica config
-cfg.method           = 'runica';
-cfg.channel          = {'all'};
-cfg.trials           = 'all';
-cfg.numcomponent     = 'all';
-cfg.demean           = 'yes';
-cfg.runica.extended  = 1;
-
-% ICA solution
-cfg.unmixing     = config.ica1.unmixing;
-cfg.topolabel    = config.ica1.topolabel;
-
-% components
-comp = ft_componentanalysis(cfg,data);
-
-% clear cfg
-clear cfg data
-
-%% remove components
-
-% cfg for rejecting components (reject: blinks, eye movements, ecg, ref)
-cfg.component = sortrows(ics2reject)';
-cfg.demean    = 'yes';
-
-% reject components
-data = ft_rejectcomponent(cfg,comp);
-
-% clear cfg
-clear cfg comp ics2reject
-
-%% remove trials
-
-% define trials to keep
-trials               = 1:length(data.trial);
-trials(trls2remove)  = [];
-
-% config for deleting trials
-cfg.trials   = trials;
-
-% remove trials
-data   = ft_preprocessing(cfg,data);
-nartfree_trials = trials;
-
-config.nartfree_trials = nartfree_trials;
-
-% clear variables
-clear cfg trials trls2remove
-
-%% remove eye & reference channels (before interpolation)
-
-cfg.channel     = {'all','-IO1','-IO2','-M1', '-M2','-VEOG','-HEOG'};
-cfg.demean      = 'yes';
-
-% remove channels
-data = ft_preprocessing(cfg,data);
-
-% clear cfg
-clear cfg
-
-% interpolation cfg
-cfg            = [];
-cfg.method     = 'spline';
-cfg.badchannel = data.label(chns2interp);
-cfg.trials     = 'all';
-cfg.lambda     = 1e-5; 
-cfg.order      = 4; 
-cfg.elec       = config.elec;
-
-% interpolate
-data = ft_channelrepair(cfg,data);
-
-% clear cfg
-clear cfg chns2interp
-
-%% keep channel x trial artifacts  
-
-data.ArtDect.channels_x_trials = config.ArtDect.channels_x_trials;
-
-%% create overview of percentage of excluded trials, update config.trl
-
-tmp_trialNumbers(1,1) = length(data.trial);
-tmp_trialNumbers(2,1) = 1200; % maximum amount of trials
-tmp_trialNumbers(3,1) = (100-((tmp_trialNumbers(1,1)/tmp_trialNumbers(2,1))*100)); % percentage of excluded trials
-config.overview_trial_numbers = tmp_trialNumbers;
-
-%% update config.trl with trigger codes
-
-% add info whether trial is included in final set; 1 = trial containing no artifact
-config.trl(:,4)                 = 0;
-config.trl(nartfree_trials, 4)  = 1;
-% add trial number
-config.trl(:,5) = 0;
-config.trl(nartfree_trials, 5)  = nartfree_trials;
-% load marker file
-mrk = config.mrk;
-for i = 1:size(mrk,2)
-   mrk_val{i,1} = mrk(1,i).value;
-end
-
-% save config
-save(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
-
-%% update event table
-
-% remove trials that were not retained during preprocessing
-
-events(config.trl(:,5)==0,:) = [];
-
-%% save data
-data_eeg = data; clear data;
-save(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_art.mat']),'data_eeg', 'events');

code/a7_prep_data_for_analysis/a7_prep_data_for_analysis.m

@@ -0,0 +1 @@
+../../.git/annex/objects/z5/25/MD5E-s4777--7dd148a073a07dba2bcc98cd27124aea.m/MD5E-s4777--7dd148a073a07dba2bcc98cd27124aea.m

code/a7_prep_data_for_analysis/a7_prep_data_for_analysis_START.sh

@@ -1,22 +0,0 @@
-#!/bin/bash
-
-fun_name="a7_prep_data_for_analysis"
-job_name="eegmp_final"
-
-mkdir ./logs
-
-rootpath="$(pwd)/../.."
-rootpath=$(builtin cd $rootpath; pwd)
-
-for subj in $(seq 1 33); do
-	echo "#!/bin/bash"                    			> job.slurm
-	echo "#SBATCH --job-name ${job_name}_${subj}" 	>> job.slurm
-	echo "#SBATCH --cpus-per-task 4"				>> job.slurm
-	echo "#SBATCH --mem 8gb" 						>> job.slurm
-	echo "#SBATCH --time 01:00:00" 					>> job.slurm
-	echo "#SBATCH --output ./logs/${job_name}_${subj}.out"			>> job.slurm
-	echo "#SBATCH --workdir ." 										>> job.slurm
-	echo "./${fun_name}_run.sh /opt/matlab/R2016b ${subj} ${rootpath}" 	>> job.slurm
-	sbatch job.slurm
-	rm -f job.slurm
-done

code/a7_prep_data_for_analysis/a7_prep_data_for_analysis_START.sh

@@ -0,0 +1 @@
+../../.git/annex/objects/p7/xV/MD5E-s860--3a0307135d8381820ea4e3aacf391d13.sh/MD5E-s860--3a0307135d8381820ea4e3aacf391d13.sh

code/a7_prep_data_for_analysis/logs/eegmp_final_1.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-001
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 373 MB
-baseline correcting data 
-scaling data with 1 over 121.131884
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1376 MB
-removing 8 components
-keeping 63 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 141 from 1200processing trial 290 from 1200processing trial 448 from 1200processing trial 608 from 1200processing trial 767 from 1200processing trial 927 from 1200processing trial 1051 from 1200processing trial 1142 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 6 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 38 MB
-preprocessing
-preprocessing trial 6 from 1081preprocessing trial 141 from 1081preprocessing trial 284 from 1081preprocessing trial 428 from 1081preprocessing trial 569 from 1081preprocessing trial 711 from 1081preprocessing trial 853 from 1081preprocessing trial 996 from 1081preprocessing trial 1081 from 1081
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 40 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 2 MB
-preprocessing
-preprocessing trial 25 from 1081preprocessing trial 58 from 1081preprocessing trial 95 from 1081preprocessing trial 132 from 1081preprocessing trial 168 from 1081preprocessing trial 206 from 1081preprocessing trial 242 from 1081preprocessing trial 279 from 1081preprocessing trial 318 from 1081preprocessing trial 355 from 1081preprocessing trial 392 from 1081preprocessing trial 430 from 1081preprocessing trial 469 from 1081preprocessing trial 507 from 1081preprocessing trial 542 from 1081preprocessing trial 578 from 1081preprocessing trial 615 from 1081preprocessing trial 651 from 1081preprocessing trial 688 from 1081preprocessing trial 726 from 1081preprocessing trial 763 from 1081preprocessing trial 801 from 1081preprocessing trial 836 from 1081preprocessing trial 874 from 1081preprocessing trial 912 from 1081preprocessing trial 950 from 1081preprocessing trial 986 from 1081preprocessing trial 1013 from 1081preprocessing trial 1043 from 1081preprocessing trial 1081 from 1081
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 4 MB
-the input is raw data with 66 channels and 1081 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 2 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1081 trials .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 3 seconds and required the additional allocation of an estimated 3 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_1.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/9W/Pk/MD5E-s9274--a72b64df9b895632fc5315f541809a4b.out/MD5E-s9274--a72b64df9b895632fc5315f541809a4b.out

code/a7_prep_data_for_analysis/logs/eegmp_final_10.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-010
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 533 MB
-baseline correcting data 
-scaling data with 1 over 70.834579
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1542 MB
-removing 16 components
-keeping 55 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 145 from 1200processing trial 293 from 1200processing trial 450 from 1200processing trial 609 from 1200processing trial 767 from 1200processing trial 925 from 1200processing trial 1052 from 1200processing trial 1155 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 6 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-preprocessing
-preprocessing trial 6 from 1036preprocessing trial 139 from 1036preprocessing trial 279 from 1036preprocessing trial 421 from 1036preprocessing trial 562 from 1036preprocessing trial 703 from 1036preprocessing trial 842 from 1036preprocessing trial 984 from 1036preprocessing trial 1036 from 1036
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 4 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 2 MB
-preprocessing
-preprocessing trial 20 from 1036preprocessing trial 51 from 1036preprocessing trial 86 from 1036preprocessing trial 122 from 1036preprocessing trial 154 from 1036preprocessing trial 191 from 1036preprocessing trial 227 from 1036preprocessing trial 263 from 1036preprocessing trial 299 from 1036preprocessing trial 335 from 1036preprocessing trial 372 from 1036preprocessing trial 408 from 1036preprocessing trial 444 from 1036preprocessing trial 482 from 1036preprocessing trial 519 from 1036preprocessing trial 556 from 1036preprocessing trial 592 from 1036preprocessing trial 627 from 1036preprocessing trial 664 from 1036preprocessing trial 699 from 1036preprocessing trial 735 from 1036preprocessing trial 772 from 1036preprocessing trial 809 from 1036preprocessing trial 845 from 1036preprocessing trial 882 from 1036preprocessing trial 918 from 1036preprocessing trial 952 from 1036preprocessing trial 988 from 1036preprocessing trial 1015 from 1036preprocessing trial 1036 from 1036
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 3 MB
-the input is raw data with 66 channels and 1036 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 2 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1036 trials ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 4 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_10.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/6X/84/MD5E-s9155--24dc3cd5c77ff49ee49f6b343935f6ac.out/MD5E-s9155--24dc3cd5c77ff49ee49f6b343935f6ac.out

code/a7_prep_data_for_analysis/logs/eegmp_final_11.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-011
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 501 MB
-baseline correcting data 
-scaling data with 1 over 66.325346
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1500 MB
-removing 9 components
-keeping 62 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 3 MB
-processing trials
-processing trial 148 from 1200processing trial 295 from 1200processing trial 454 from 1200processing trial 613 from 1200processing trial 772 from 1200processing trial 931 from 1200processing trial 1053 from 1200processing trial 1145 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 8 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-preprocessing
-preprocessing trial 6 from 1108preprocessing trial 143 from 1108preprocessing trial 285 from 1108preprocessing trial 427 from 1108preprocessing trial 568 from 1108preprocessing trial 710 from 1108preprocessing trial 851 from 1108preprocessing trial 993 from 1108preprocessing trial 1108 from 1108
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 2 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 3 MB
-preprocessing
-preprocessing trial 32 from 1108preprocessing trial 65 from 1108preprocessing trial 97 from 1108preprocessing trial 133 from 1108preprocessing trial 169 from 1108preprocessing trial 207 from 1108preprocessing trial 243 from 1108preprocessing trial 280 from 1108preprocessing trial 317 from 1108preprocessing trial 354 from 1108preprocessing trial 391 from 1108preprocessing trial 426 from 1108preprocessing trial 463 from 1108preprocessing trial 501 from 1108preprocessing trial 537 from 1108preprocessing trial 573 from 1108preprocessing trial 608 from 1108preprocessing trial 645 from 1108preprocessing trial 681 from 1108preprocessing trial 717 from 1108preprocessing trial 754 from 1108preprocessing trial 791 from 1108preprocessing trial 828 from 1108preprocessing trial 866 from 1108preprocessing trial 902 from 1108preprocessing trial 938 from 1108preprocessing trial 975 from 1108preprocessing trial 1007 from 1108preprocessing trial 1025 from 1108preprocessing trial 1057 from 1108preprocessing trial 1095 from 1108preprocessing trial 1108 from 1108
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 4 MB
-the input is raw data with 66 channels and 1108 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 2 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1108 trials ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 5 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_11.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/KM/Qv/MD5E-s9368--8aa16d1e0f14aaef9bbd1fd7a9871a69.out/MD5E-s9368--8aa16d1e0f14aaef9bbd1fd7a9871a69.out

code/a7_prep_data_for_analysis/logs/eegmp_final_12.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-012
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 436 MB
-baseline correcting data 
-scaling data with 1 over 165.875505
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 5 seconds and required the additional allocation of an estimated 1440 MB
-removing 17 components
-keeping 54 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 146 from 1200processing trial 295 from 1200processing trial 453 from 1200processing trial 613 from 1200processing trial 774 from 1200processing trial 934 from 1200processing trial 1059 from 1200processing trial 1162 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 6 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 43 MB
-preprocessing
-preprocessing trial 6 from 1086preprocessing trial 139 from 1086preprocessing trial 279 from 1086preprocessing trial 421 from 1086preprocessing trial 560 from 1086preprocessing trial 701 from 1086preprocessing trial 842 from 1086preprocessing trial 984 from 1086preprocessing trial 1069 from 1086preprocessing trial 1086 from 1086
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 44 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 4 MB
-preprocessing
-preprocessing trial 26 from 1086preprocessing trial 63 from 1086preprocessing trial 99 from 1086preprocessing trial 135 from 1086preprocessing trial 170 from 1086preprocessing trial 206 from 1086preprocessing trial 242 from 1086preprocessing trial 278 from 1086preprocessing trial 313 from 1086preprocessing trial 349 from 1086preprocessing trial 387 from 1086preprocessing trial 425 from 1086preprocessing trial 460 from 1086preprocessing trial 498 from 1086preprocessing trial 535 from 1086preprocessing trial 573 from 1086preprocessing trial 610 from 1086preprocessing trial 645 from 1086preprocessing trial 681 from 1086preprocessing trial 717 from 1086preprocessing trial 754 from 1086preprocessing trial 791 from 1086preprocessing trial 828 from 1086preprocessing trial 864 from 1086preprocessing trial 902 from 1086preprocessing trial 938 from 1086preprocessing trial 975 from 1086preprocessing trial 1007 from 1086preprocessing trial 1033 from 1086preprocessing trial 1071 from 1086preprocessing trial 1086 from 1086
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 6 MB
-the input is raw data with 66 channels and 1086 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 1 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1086 trials ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 3 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_12.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/wx/4P/MD5E-s9338--92ce231c29aad67df609363a95352daa.out/MD5E-s9338--92ce231c29aad67df609363a95352daa.out

code/a7_prep_data_for_analysis/logs/eegmp_final_13.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-013
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 494 MB
-baseline correcting data 
-scaling data with 1 over 203.456122
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1497 MB
-removing 12 components
-keeping 59 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 145 from 1200processing trial 293 from 1200processing trial 450 from 1200processing trial 609 from 1200processing trial 768 from 1200processing trial 927 from 1200processing trial 1053 from 1200processing trial 1155 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 8 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 45 MB
-preprocessing
-preprocessing trial 6 from 1082preprocessing trial 141 from 1082preprocessing trial 283 from 1082preprocessing trial 426 from 1082preprocessing trial 569 from 1082preprocessing trial 712 from 1082preprocessing trial 855 from 1082preprocessing trial 996 from 1082preprocessing trial 1082 from 1082
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 45 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 4 MB
-preprocessing
-preprocessing trial 28 from 1082preprocessing trial 66 from 1082preprocessing trial 101 from 1082preprocessing trial 137 from 1082preprocessing trial 174 from 1082preprocessing trial 210 from 1082preprocessing trial 248 from 1082preprocessing trial 285 from 1082preprocessing trial 323 from 1082preprocessing trial 359 from 1082preprocessing trial 396 from 1082preprocessing trial 434 from 1082preprocessing trial 470 from 1082preprocessing trial 508 from 1082preprocessing trial 545 from 1082preprocessing trial 583 from 1082preprocessing trial 620 from 1082preprocessing trial 657 from 1082preprocessing trial 695 from 1082preprocessing trial 733 from 1082preprocessing trial 770 from 1082preprocessing trial 807 from 1082preprocessing trial 842 from 1082preprocessing trial 880 from 1082preprocessing trial 917 from 1082preprocessing trial 955 from 1082preprocessing trial 991 from 1082preprocessing trial 1016 from 1082preprocessing trial 1045 from 1082preprocessing trial 1082 from 1082
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 6 MB
-the input is raw data with 66 channels and 1082 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 3 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1082 trials ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 3 seconds and required the additional allocation of an estimated 3 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_13.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/zW/Qx/MD5E-s9274--78a6290c980a67563bb425dc038278b5.out/MD5E-s9274--78a6290c980a67563bb425dc038278b5.out

code/a7_prep_data_for_analysis/logs/eegmp_final_14.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-014
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 563 MB
-baseline correcting data 
-scaling data with 1 over 262.522723
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1572 MB
-removing 16 components
-keeping 55 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 144 from 1200processing trial 289 from 1200processing trial 443 from 1200processing trial 597 from 1200processing trial 748 from 1200processing trial 901 from 1200processing trial 1035 from 1200processing trial 1137 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 8 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-preprocessing
-preprocessing trial 6 from 965preprocessing trial 139 from 965preprocessing trial 278 from 965preprocessing trial 415 from 965preprocessing trial 552 from 965preprocessing trial 691 from 965preprocessing trial 831 from 965preprocessing trial 965 from 965
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 2 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 4 MB
-preprocessing
-preprocessing trial 35 from 965preprocessing trial 59 from 965preprocessing trial 82 from 965preprocessing trial 106 from 965preprocessing trial 131 from 965preprocessing trial 151 from 965preprocessing trial 171 from 965preprocessing trial 191 from 965preprocessing trial 212 from 965preprocessing trial 236 from 965preprocessing trial 254 from 965preprocessing trial 276 from 965preprocessing trial 312 from 965preprocessing trial 350 from 965preprocessing trial 387 from 965preprocessing trial 425 from 965preprocessing trial 463 from 965preprocessing trial 498 from 965preprocessing trial 536 from 965preprocessing trial 574 from 965preprocessing trial 610 from 965preprocessing trial 646 from 965preprocessing trial 683 from 965preprocessing trial 719 from 965preprocessing trial 757 from 965preprocessing trial 795 from 965preprocessing trial 833 from 965preprocessing trial 869 from 965preprocessing trial 904 from 965preprocessing trial 942 from 965preprocessing trial 965 from 965
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 5 MB
-the input is raw data with 66 channels and 965 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 2 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 965 trials .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 1 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_14.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/8v/8Z/MD5E-s9059--aa1a4d73d87b0fd4c5b0f0d657b2663c.out/MD5E-s9059--aa1a4d73d87b0fd4c5b0f0d657b2663c.out

code/a7_prep_data_for_analysis/logs/eegmp_final_15.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-015
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 513 MB
-baseline correcting data 
-scaling data with 1 over 178.474136
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1518 MB
-removing 16 components
-keeping 55 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 142 from 1200processing trial 286 from 1200processing trial 440 from 1200processing trial 595 from 1200processing trial 750 from 1200processing trial 905 from 1200processing trial 1037 from 1200processing trial 1140 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 8 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 46 MB
-preprocessing
-preprocessing trial 6 from 1009preprocessing trial 137 from 1009preprocessing trial 276 from 1009preprocessing trial 416 from 1009preprocessing trial 555 from 1009preprocessing trial 694 from 1009preprocessing trial 833 from 1009preprocessing trial 972 from 1009preprocessing trial 1009 from 1009
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 47 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 2 MB
-preprocessing
-preprocessing trial 18 from 1009preprocessing trial 48 from 1009preprocessing trial 83 from 1009preprocessing trial 120 from 1009preprocessing trial 156 from 1009preprocessing trial 190 from 1009preprocessing trial 225 from 1009preprocessing trial 262 from 1009preprocessing trial 299 from 1009preprocessing trial 335 from 1009preprocessing trial 372 from 1009preprocessing trial 409 from 1009preprocessing trial 447 from 1009preprocessing trial 483 from 1009preprocessing trial 520 from 1009preprocessing trial 556 from 1009preprocessing trial 591 from 1009preprocessing trial 626 from 1009preprocessing trial 662 from 1009preprocessing trial 698 from 1009preprocessing trial 736 from 1009preprocessing trial 771 from 1009preprocessing trial 808 from 1009preprocessing trial 844 from 1009preprocessing trial 880 from 1009preprocessing trial 916 from 1009preprocessing trial 953 from 1009preprocessing trial 988 from 1009preprocessing trial 1009 from 1009
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 3 MB
-the input is raw data with 66 channels and 1009 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 3 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1009 trials .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 3 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_15.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/jJ/GQ/MD5E-s9123--23054e0fd5ccd792d1f044b3638c8c41.out/MD5E-s9123--23054e0fd5ccd792d1f044b3638c8c41.out

code/a7_prep_data_for_analysis/logs/eegmp_final_16.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-016
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 551 MB
-baseline correcting data 
-scaling data with 1 over 144.129731
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1559 MB
-removing 11 components
-keeping 60 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 3 MB
-processing trials
-processing trial 139 from 1200processing trial 285 from 1200processing trial 440 from 1200processing trial 595 from 1200processing trial 751 from 1200processing trial 903 from 1200processing trial 1037 from 1200processing trial 1139 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 9 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-preprocessing
-preprocessing trial 6 from 1043preprocessing trial 137 from 1043preprocessing trial 275 from 1043preprocessing trial 416 from 1043preprocessing trial 555 from 1043preprocessing trial 696 from 1043preprocessing trial 837 from 1043preprocessing trial 978 from 1043preprocessing trial 1043 from 1043
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 2 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 2 MB
-preprocessing
-preprocessing trial 18 from 1043preprocessing trial 52 from 1043preprocessing trial 85 from 1043preprocessing trial 121 from 1043preprocessing trial 158 from 1043preprocessing trial 196 from 1043preprocessing trial 232 from 1043preprocessing trial 268 from 1043preprocessing trial 303 from 1043preprocessing trial 340 from 1043preprocessing trial 374 from 1043preprocessing trial 410 from 1043preprocessing trial 447 from 1043preprocessing trial 483 from 1043preprocessing trial 519 from 1043preprocessing trial 554 from 1043preprocessing trial 590 from 1043preprocessing trial 626 from 1043preprocessing trial 662 from 1043preprocessing trial 699 from 1043preprocessing trial 735 from 1043preprocessing trial 770 from 1043preprocessing trial 807 from 1043preprocessing trial 843 from 1043preprocessing trial 879 from 1043preprocessing trial 917 from 1043preprocessing trial 953 from 1043preprocessing trial 989 from 1043preprocessing trial 1016 from 1043preprocessing trial 1043 from 1043
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 4 MB
-the input is raw data with 66 channels and 1043 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 3 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1043 trials ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 5 MB

code/a7_prep_data_for_analysis/logs/eegmp_final_16.out

@@ -0,0 +1 @@
+../../../.git/annex/objects/1F/9Q/MD5E-s9231--51830669389d4eb5c3d84f15a09ddefd.out/MD5E-s9231--51830669389d4eb5c3d84f15a09ddefd.out

code/a7_prep_data_for_analysis/logs/eegmp_final_17.out

@@ -1,114 +0,0 @@
-------------------------------------------
-Setting up environment variables
----
-LD_LIBRARY_PATH is .:/opt/matlab/R2016b/runtime/glnxa64:/opt/matlab/R2016b/bin/glnxa64:/opt/matlab/R2016b/sys/os/glnxa64:/opt/matlab/R2016b/sys/opengl/lib/glnxa64
-processing ID sub-017
-the input is raw data with 72 channels and 1200 trials
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 784
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/getdimord.m' at line 734
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/private/makessense.m' at line 41
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_datatype_raw.m' at line 90
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/utilities/ft_checkdata.m' at line 277
- In '/mnt/beegfs/home/kosciessa/.mcrCache9.1/a7_pre0/mnt/beegfs/home/kosciessa/EEGManyPipelines/eegmp_preproc/tools/fieldtrip/ft_componentanalysis.m' at line 185
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-Warning: could not determine dimord of "chanlocs" in:
-
-         hdr: [1x1 struct]
-     fsample: 500
-       trial: {1x1200 cell}
-        time: {1x1200 cell}
-       label: {72x1 cell}
-         cfg: [1x1 struct]
-        elec: [1x1 struct]
-    chanlocs: [1x72 struct]
-
-
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 543 MB
-baseline correcting data 
-scaling data with 1 over 113.734056
-not concatenating data
-starting decomposition using predetermined unmixing matrix
-also applying the unmixing matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_componentanalysis" took 6 seconds and required the additional allocation of an estimated 1543 MB
-removing 14 components
-keeping 57 components
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-processing trials
-processing trial 140 from 1200processing trial 284 from 1200processing trial 438 from 1200processing trial 593 from 1200processing trial 748 from 1200processing trial 902 from 1200processing trial 1036 from 1200processing trial 1130 from 1200processing trial 1200 from 1200
-also applying the backprojection matrix to the elec structure
-Warning: copying input chantype to montage
-Warning: copying input chanunit to montage
-the call to "ft_rejectcomponent" took 3 seconds and required the additional allocation of an estimated 8 MB
-Warning: sampleinfo in the configuration is inconsistent with the actual data
-Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 1 MB
-preprocessing
-preprocessing trial 6 from 1006preprocessing trial 138 from 1006preprocessing trial 277 from 1006preprocessing trial 417 from 1006preprocessing trial 556 from 1006preprocessing trial 695 from 1006preprocessing trial 835 from 1006preprocessing trial 973 from 1006preprocessing trial 1006 from 1006
-the call to "ft_preprocessing" took 1 seconds and required the additional allocation of an estimated 2 MB
-the call to "ft_selectdata" took 1 seconds and required the additional allocation of an estimated 2 MB
-preprocessing
-preprocessing trial 27 from 1006preprocessing trial 56 from 1006preprocessing trial 91 from 1006preprocessing trial 128 from 1006preprocessing trial 165 from 1006preprocessing trial 201 from 1006preprocessing trial 237 from 1006preprocessing trial 272 from 1006preprocessing trial 308 from 1006preprocessing trial 344 from 1006preprocessing trial 381 from 1006preprocessing trial 418 from 1006preprocessing trial 456 from 1006preprocessing trial 491 from 1006preprocessing trial 528 from 1006preprocessing trial 564 from 1006preprocessing trial 600 from 1006preprocessing trial 636 from 1006preprocessing trial 671 from 1006preprocessing trial 707 from 1006preprocessing trial 744 from 1006preprocessing trial 780 from 1006preprocessing trial 814 from 1006preprocessing trial 851 from 1006preprocessing trial 888 from 1006preprocessing trial 923 from 1006preprocessing trial 960 from 1006preprocessing trial 997 from 1006preprocessing trial 1006 from 1006
-the call to "ft_preprocessing" took 4 seconds and required the additional allocation of an estimated 3 MB
-the input is raw data with 66 channels and 1006 trials
-the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 0 MB
-assuming that the data is EEG, use cfg.senstype to overrule this
-Your data and configuration allow for multiple sensor definitions.
-Warning: using electrodes specified in the configuration\n
-There are 3 bad channels
-There are 0 missing channels
-Spherical spline and surface Laplacian interpolation will treat bad and missing channels the same. Missing channels will be concatenated at the end of your data structure.
-Checking spherical fit... perfect spherical fit (residual: 0.0%)
-computing weight matrix... done!
-
-interpolating channels for 1006 trials ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
-the call to "ft_channelrepair" took 2 seconds and required the additional allocation of an estimated 3 MB