Added example dataset for annotations and nested derivatives.

eeg_face13/README

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+# Face13 Dataset
+
+Data used for JofV Deconstructing the early visual electrocortical response to face and house stimuli:
+https://jov.arvojournals.org/article.aspx?articleid=2121634

eeg_face13/code/BIDS-Init-Face13-EEGLAB/README.md

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+# BIDS-Init-Face13-EEGLAB
+Root BIDS level initialization and BIDSification tool suite
+
+## How to Run
+This installation assumes familiarity with the bash terminal, paths, and Matlab console use.
+1. Download Face13 sourcedata folder, [here](https://drive.google.com/open?id=1xq85woDpAYXhCtzdgjkXpjjjggiWSKtc)
+2. Create a project folder: `mkdir Face13`
+3. Move the sourcedata into the project folder and rename as `sourcedata`. This step may differ based on download location and platform.
+4. Enter the project folder: `cd Face13`
+5. Create a code folder: `mkdir code`
+6. Enter code folder: `cd code`
+7. Use: `git clone --recursive https://github.com/BUCANL/BIDS-Init-Face13-EEGLAB.git` inside of the code folder
+8. Point Matlab to project folder. In our case, Face13.
+9. In the Matlab console execute: `addpath code/BIDS-Init-Face13-EEGLAB`
+10. In the Matlab console execute: `addpath code/BIDS-Init-Face13-EEGLAB/eeglab`
+11. In the Matlab console execute: `eeglab`
+12. At this point the familiar eeglab window should appear.
+13. To merge and relabel bdf files run: `init_script.m`
+14. To BIDSify run: `bids_face13.m`
+15. Select the project directory with the file chooser
+16. Visualize your data!

eeg_face13/code/BIDS-Init-Face13-EEGLAB/bids_face13.m

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+% Global settings
+bidsOpt.FileExt = 'edf';
+bidsOpt.InteralUse = true;
+
+% Data
+data(1).file = {'./sourcedata/eeg/sub-s01_task-faceFO_eeg.set'};
+data(1).session = 1;
+data(1).run = 1;
+
+data(2).file = {'./sourcedata/eeg/sub-s02_task-faceFO_eeg.set'};
+data(2).session = 1;
+data(2).run = 1;
+
+data(3).file = {'./sourcedata/eeg/sub-s03_task-faceFO_eeg.set'};
+data(3).session = 1;
+data(3).run = 1;
+
+data(4).file = {'./sourcedata/eeg/sub-s04_task-faceFO_eeg.set'};
+data(4).session = 1;
+data(4).run = 1;
+
+data(5).file = {'./sourcedata/eeg/sub-s05_task-faceFO_eeg.set'};
+data(5).session = 1;
+data(5).run = 1;
+
+data(6).file = {'./sourcedata/eeg/sub-s06_task-faceFO_eeg.set'};
+data(6).session = 1;
+data(6).run = 1;
+
+data(7).file = {'./sourcedata/eeg/sub-s07_task-faceFO_eeg.set'};
+data(7).session = 1;
+data(7).run = 1;
+
+data(8).file = {'./sourcedata/eeg/sub-s08_task-faceFO_eeg.set'};
+data(8).session = 1;
+data(8).run = 1;
+
+data(9).file = {'./sourcedata/eeg/sub-s09_task-faceFO_eeg.set'};
+data(9).session = 1;
+data(9).run = 1;
+
+data(10).file = {'./sourcedata/eeg/sub-s10_task-faceFO_eeg.set'};
+data(10).session = 1;
+data(10).run = 1;
+
+% general information for dataset_description.json file
+% -----------------------------------------------------
+generalInfo.Name = 'faceFO';
+generalInfo.License = 'ODbL (https://opendatacommons.org/licenses/odbl/summary/)';
+generalInfo.Authors = {'James A. Desjardins', 'Sidney J. Segalowitz'};
+generalInfo.HowToAcknowledge = 'Desjardins, J. A., & Segalowitz, S. J. (2013). Deconstructing the early visual electrocortical responses to face and house stimuli. Journal of Vision, 13(5), 22-22.';
+generalInfo.Funding = {'NSERC funding to Sidney Segalowitz'};
+generalInfo.ReferencesAndLinks = {'http://jov.arvojournals.org/article.aspx?articleid=2121634'};
+generalInfo.DatasetDOI = '10.1167/13.5.22';
+
+% Readme and changes
+% -----------------------------------------------------
+README = sprintf('# Face13 Dataset\n\nData used for JofV Deconstructing the early visual electrocortical response to face and house stimuli:\nhttps://jov.arvojournals.org/article.aspx?articleid=2121634');
+% CHANGES = sprintf();
+
+% Task information for xxxx-eeg.json file
+% -----------------------------------------------------
+tInfo.TaskName = 'FaceHouseCheck';
+tInfo.TaskDescription = 'Visual presentation of oval cropped face and house images both upright and inverted. Rare left or right half oval checkerboards were presetned as targets for keypress response.';
+tInfo.InstitutionName =  'Brock University';
+tInfo.InstitutionAddress = '500 Glenridge Ave, St.Catharines, Ontario';
+tInfo.EOGChannelCount =  7;
+tInfo.EMGChannelCount =  0;
+tInfo.MiscChannelCount =  0;
+tInfo.TriggerChannelCount = 0;
+tInfo.PowerLineFrequency = 60;
+tInfo.EEGPlacementScheme = 'Custom equidistant 128 channel BioSemi montage established in coordination with Judith Schedden McMaster Univertisy';
+tInfo.Manufacturer = 'BioSemi';
+tInfo.ManufacturersModelName = 'ActiveTwo';
+tInfo.HardwareFilters = 'n/a';
+tInfo.SoftwareFilters = 'n/a';
+tInfo.SoftwareVersions = 'NI ActiView 532-Lores';
+tInfo.CapManufacturer = 'ElectroCap International';
+tInfo.CapManufacturersModelName = '10032';
+
+% channel location file
+% ---------------------
+chanlocs = 'sourcedata/misc/BioSemi_BUCANL_EEGLAB.sfp';
+
+% coordsystem string
+% This string will be placed in each coordsystem.json
+% ---------------------
+coordsys = '{"EEGCoordinateSystem":"Other","EEGCoordinateUnits":"metres"}';
+
+% call to the export function
+% ---------------------------
+bids_export(data, 'targetdir', uigetdir, 'taskName', ...
+    generalInfo.Name, 'gInfo', generalInfo, 'coordsys', coordsys, ...
+    'chanlocs', chanlocs, 'README', README, 'bidsOpt', bidsOpt,'tInfo',tInfo);
+
+disp('Done');
+
+% bids_export(data, 'targetdir', '/Users/arno/temp/bids_meditation_export', 'taskName', ...
+%     'meditation', 'trialtype', trialTypes, 'gInfo', generalInfo, 'pInfo', pInfo, ...
+%     'pInfoDesc', pInfoDesc, 'eInfoDesc', eInfoDesc, 'README', README, ...
+%     'CHANGES', CHANGES, 'stimuli', stimuli, 'codefiles', code, 'tInfo', tInfo, 'chanlocs', chanlocs);
+
+
+% init_bids_sub_script('.','',... 'TaskName', 'FaceHouseCheck', ... 'TaskDescription', 'Visual presentation of oval cropped face and house images both upright and inverted. Rare left or right half oval checkerboards were presetned as targets for keypress response.', ... 'InstitutionName', 'Brock University', ... 'InstitutionAddress', '500 Glenridge Ave, St.Catharines, Ontario', ... 'EOGChannelCount', 7, ... 'EMGChannelCount', 0, ... 'MiscChannelCount', 0, ... 'TriggerChannelCount', 0, ... 'PowerLineFrequency', 60, ... 'EEGPlacementScheme', 'Custom equidistant 128 channel BioSemi montage established in coordination with Judith Schedden McMaster Univertisy', ... 'Manufacturer', 'BioSemi', ... 'ManufacturersModelName', 'ActiveTwo', ... 'HardwareFilters', 'n/a', ... 'SoftwareFilters', 'n/a', ... 'SoftwareVersions', 'NI ActiView 532-Lores', ... 'CapManufacturer', 'ElectroCap International', ... 'CapManufacturersModelName', '10032');
+

eeg_face13/code/BIDS-Init-Face13-EEGLAB/bids_face13_min.m

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+% Preface:
+
+% Global settings
+bidsOpt.FileExt = 'edf';
+bidsOpt.InteralUse = true;
+
+data(1).file = {'./sourcedata/eeg/sub-s01_task-faceFO_eeg.set'};
+data(1).session = 1;
+data(1).run     = 1;
+
+% general information for dataset_description.json file
+% -----------------------------------------------------
+generalInfo.Name = 'faceFO';
+generalInfo.License = 'ODbL (https://opendatacommons.org/licenses/odbl/summary/)';
+generalInfo.Authors = {'James A. Desjardins', 'Sidney J. Segalowitz'};
+generalInfo.HowToAcknowledge = 'Desjardins, J. A., & Segalowitz, S. J. (2013). Deconstructing the early visual electrocortical responses to face and house stimuli. Journal of Vision, 13(5), 22-22.';
+generalInfo.Funding = {'NSERC funding to Sidney Segalowitz'};
+generalInfo.ReferencesAndLinks = {'http://jov.arvojournals.org/article.aspx?articleid=2121634'};
+generalInfo.DatasetDOI = '10.1167/13.5.22';
+
+README = sprintf('# Face13 Dataset\n\nData used for JofV Deconstructing the early visual electrocortical response to face and house stimuli:\nhttps://jov.arvojournals.org/article.aspx?articleid=2121634');
+
+% Task information for xxxx-eeg.json file
+% -----------------------------------------------------
+tInfo.TaskName = 'FaceHouseCheck';
+tInfo.TaskDescription = 'Visual presentation of oval cropped face and house images both upright and inverted. Rare left or right half oval checkerboards were presetned as targets for keypress response.';
+tInfo.InstitutionName =  'Brock University';
+tInfo.InstitutionAddress = '500 Glenridge Ave, St.Catharines, Ontario';
+tInfo.EOGChannelCount =  7;
+tInfo.EMGChannelCount =  0;
+tInfo.MiscChannelCount =  0;
+tInfo.TriggerChannelCount = 0;
+tInfo.PowerLineFrequency = 60;
+tInfo.EEGPlacementScheme = 'Custom equidistant 128 channel BioSemi montage established in coordination with Judith Schedden McMaster Univertisy';
+tInfo.Manufacturer = 'BioSemi';
+tInfo.ManufacturersModelName = 'ActiveTwo';
+tInfo.HardwareFilters = 'n/a';
+tInfo.SoftwareFilters = 'n/a';
+tInfo.SoftwareVersions = 'NI ActiView 532-Lores';
+tInfo.CapManufacturer = 'ElectroCap International';
+tInfo.CapManufacturersModelName = '10032';
+
+% channel location file
+% ---------------------
+chanlocs = './sourcedata/misc/BioSemi_BUCANL_EEGLAB.sfp';
+
+% coordsystem string
+% This string will be placed in each coordsystem.json
+% ---------------------
+coordsys = '{"EEGCoordinateSystem":"Other","EEGCoordinateUnits":"metres"}';
+
+% call to the export function
+% ---------------------------
+bids_export(data, 'targetdir', uigetdir, 'taskName', ...
+    generalInfo.Name, 'gInfo', generalInfo, 'coordsys', coordsys, ...
+    'chanlocs', chanlocs, 'README', README, 'bidsOpt', bidsOpt,'tInfo',tInfo);
+
+disp('Done!');
+
+% bids_export(data, 'targetdir', '/Users/arno/temp/bids_meditation_export', 'taskName', ...
+%     'meditation', 'trialtype', trialTypes, 'gInfo', generalInfo, 'pInfo', pInfo, ...
+%     'pInfoDesc', pInfoDesc, 'eInfoDesc', eInfoDesc, 'README', README, ...
+%     'CHANGES', CHANGES, 'stimuli', stimuli, 'codefiles', code, 'tInfo', tInfo, 'chanlocs', chanlocs);

eeg_face13/code/BIDS-Init-Face13-EEGLAB/eeg_init.m

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+function eeg_init(inbdffiles,outsetfile)
+
+%loop through inbdffiles
+for i=1:length(inbdffiles);
+    %import bdf file
+    ALLEEG(i) = pop_biosig(inbdffiles{i}, 'channels', 1:128 );
+
+    %resample to 512
+    ALLEEG(i) = pop_resample( ALLEEG(i), 512);
+end
+
+%merge files
+EEG = pop_mergeset( ALLEEG, 1:length(ALLEEG), 0);
+
+%load average BUCANL BioSemi head channel coordinates
+EEG=pop_chanedit(EEG, 'load',{'sourcedata/misc/BioSemi_BUCANL_EEGLAB.sfp' 'filetype' 'autodetect'});
+
+% Make sure each channel has the EEG type written in it for future BIDS
+for i=1:length(EEG.chanlocs)
+    EEG.chanlocs(i).type = 'eeg';
+end
+
+%rename events
+for i=1:length(EEG.event);
+    if isnumeric(EEG.event(i).type);
+        EEG.event(i).type=num2str(EEG.event(i).type);
+    end
+    if strcmp(EEG.event(i).type,'11');
+        EEG.event(i).type='house-upright-f1';
+    elseif strcmp(EEG.event(i).type,'12');
+        EEG.event(i).type='house-upright-f2';
+    elseif strcmp(EEG.event(i).type,'13');
+        EEG.event(i).type='house-upright-f3';
+    elseif strcmp(EEG.event(i).type,'14');
+        EEG.event(i).type='house-upright-f4';
+    elseif strcmp(EEG.event(i).type,'15');
+        EEG.event(i).type='house-upright-f5';
+    elseif strcmp(EEG.event(i).type,'16');
+        EEG.event(i).type='house-upright-f6';
+    elseif strcmp(EEG.event(i).type,'21');
+        EEG.event(i).type='house-inverted-f1';
+    elseif strcmp(EEG.event(i).type,'22');
+        EEG.event(i).type='house-inverted-f2';
+    elseif strcmp(EEG.event(i).type,'23');
+        EEG.event(i).type='house-inverted-f3';
+    elseif strcmp(EEG.event(i).type,'24');
+        EEG.event(i).type='house-inverted-f4';
+    elseif strcmp(EEG.event(i).type,'25');
+        EEG.event(i).type='house-inverted-f5';
+    elseif strcmp(EEG.event(i).type,'26');
+        EEG.event(i).type='house-inverted-f6';
+    elseif strcmp(EEG.event(i).type,'31');
+        EEG.event(i).type='face-upright-f1';
+    elseif strcmp(EEG.event(i).type,'32');
+        EEG.event(i).type='face-upright-f2';
+    elseif strcmp(EEG.event(i).type,'33');
+        EEG.event(i).type='face-upright-f3';
+    elseif strcmp(EEG.event(i).type,'34');
+        EEG.event(i).type='face-upright-f4';
+    elseif strcmp(EEG.event(i).type,'35');
+        EEG.event(i).type='face-upright-f5';
+    elseif strcmp(EEG.event(i).type,'36');
+        EEG.event(i).type='face-upright-f6';
+    elseif strcmp(EEG.event(i).type,'41');
+        EEG.event(i).type='face-inverted-f1';
+    elseif strcmp(EEG.event(i).type,'42');
+        EEG.event(i).type='face-inverted-f2';
+    elseif strcmp(EEG.event(i).type,'43');
+        EEG.event(i).type='face-inverted-f3';
+    elseif strcmp(EEG.event(i).type,'44');
+        EEG.event(i).type='face-inverted-f4';
+    elseif strcmp(EEG.event(i).type,'45');
+        EEG.event(i).type='face-inverted-f5';
+    elseif strcmp(EEG.event(i).type,'46');
+        EEG.event(i).type='face-inverted-f6';
+    elseif strcmp(EEG.event(i).type,'51');
+        EEG.event(i).type='checker-f1';
+    elseif strcmp(EEG.event(i).type,'52');
+        EEG.event(i).type='checker-f2';
+    elseif strcmp(EEG.event(i).type,'53');
+        EEG.event(i).type='checker-f3';
+    elseif strcmp(EEG.event(i).type,'54');
+        EEG.event(i).type='checker-f4';
+    elseif strcmp(EEG.event(i).type,'55');
+        EEG.event(i).type='checker-f5';
+    elseif strcmp(EEG.event(i).type,'56');
+        EEG.event(i).type='checker-f6';
+    elseif strcmp(EEG.event(i).type,'211');
+        EEG.event(i).type='face-upright';
+    elseif strcmp(EEG.event(i).type,'212');
+        EEG.event(i).type='face-inverted';
+    elseif strcmp(EEG.event(i).type,'213');
+        EEG.event(i).type='house-upright';
+    elseif strcmp(EEG.event(i).type,'214');
+        EEG.event(i).type='house-inverted';
+    elseif strcmp(EEG.event(i).type,'215');
+        EEG.event(i).type='checker-left';
+    elseif strcmp(EEG.event(i).type,'216');
+        EEG.event(i).type='checker-right';
+    elseif strcmp(EEG.event(i).type,'201');
+        EEG.event(i).type='press-left';
+    elseif strcmp(EEG.event(i).type,'204');
+        EEG.event(i).type='press-right';
+    elseif strcmp(EEG.event(i).type,'boundary');
+        EEG.event(i).duration=0;
+    else
+        EEG.event(i).type=['e-',num2str(EEG.event(i).type)];
+    end
+end
+
+% Special casing for parallel port issue
+if strcmp(outsetfile,'sourcedata/eeg/sub-s07_task-faceFO_eeg.set')
+    eind=find([EEG.event.latency]>789010 & [EEG.event.latency]<828844);
+    reAccum = [];
+    for i=1:length(eind)
+        if ~strcmp(EEG.event(eind(i)).type,'boundary')
+            reAccum = [reAccum; eind(i)];
+        end
+    end
+    EEG.event(reAccum) = [];
+end
+
+%save output set file
+EEG = pop_saveset( EEG, 'filename',outsetfile);
+
+