hello,
So i have been able to import the data in Brainstorm using the following script :
The script is using GitHub - kwikteam/npy-matlab: Experimental code to read/write NumPy .NPY files in MATLAB · GitHub to load the npy data.
% Script to import data from coreg-spikes
bids_data_folder = {'/Users/edelaire1/Downloads/coreg-spikes'};
selectsubj = {'sub-01','sub-02','sub-03','sub-04','sub-05','sub-06','sub-07','sub-08'};
% Start a new report
bst_report('Start', []);
% Process: Import BIDS dataset
sFiles = bst_process('CallProcess', 'process_import_bids', [], [], ...
'bidsdir', {bids_data_folder(1), 'BIDS'}, ...
'selectsubj', strjoin(selectsubj,','), ...
'nvertices', 15000, ...
'mni', 'maff8', ... % Linear
'anatregister', 'spm12', ... % SPM12
'groupsessions', 1, ...
'channelalign', 1);
for iSubject = 1:length(selectsubj)
fprintf('Importing data of subject %s \n',selectsubj{iSubject})
data_folder = fullfile("derivatives/","epochs/",selectsubj{iSubject});
iEEG_folder = fullfile(data_folder,"ieeg");
EEG_folder = fullfile(data_folder,"eeg");
json_EEG = bst_jsondecode(fullfile(EEG_folder,sprintf("%s_coordsystem.json",selectsubj{iSubject} ) ));
sFid = process_import_bids('GetFiducials',json_EEG, 'mm');
electrodes_file = fullfile(EEG_folder, sprintf('%s_electrodes.tsv',selectsubj{iSubject} ));
% Create new study
iStudy = db_add_condition(selectsubj{iSubject}, 'EEG');
sStudy = bst_get('Study', iStudy);
% Load Channels
channel_info = in_tsv(fullfile(EEG_folder, sprintf('%s_task-rest_run-01_channels.tsv', selectsubj{iSubject})));
electrodes_info = in_tsv(fullfile(EEG_folder, sprintf('%s_electrodes.tsv', selectsubj{iSubject})));
nChan = size(channel_info,1);
factor = 0.001;
ChannelMat = db_template('channelmat');
ChannelMat.Comment = 'BIDS channels';
ChannelMat.Channel = repmat(db_template('channeldesc'), [1, nChan+1]);
[ChannelMat.Channel.Loc] = deal([0;0;0]);
ChannelMat.SCS.NAS = sFid.NAS;
ChannelMat.SCS.LPA = sFid.LPA;
ChannelMat.SCS.RPA = sFid.RPA;
for iChan = 1:nChan
% Name
ChannelMat.Channel(iChan).Name = electrodes_info{iChan,1};
% Type
ChannelMat.Channel(iChan).Type = 'EEG';
% Loc
ChannelMat.Channel(iChan).Loc = [str2num(electrodes_info{iChan,2}); str2num(electrodes_info{iChan,3}); str2num(electrodes_info{iChan,4})] .* factor;
% other
ChannelMat.Channel(iChan).Orient = [];
ChannelMat.Channel(iChan).Weight = 1;
ChannelMat.Channel(iChan).Comment = [];
end
electrodes_info_SEEG = in_tsv(fullfile(iEEG_folder, sprintf('%s_space-T1w_electrodes.tsv', selectsubj{iSubject})));
ChannelMat.Channel(end).Name = electrodes_info_SEEG{1,1};
ChannelMat.Channel(end).Type = 'SEEG';
ChannelMat.Channel(end).Loc = [str2num(electrodes_info_SEEG{1,2}); str2num(electrodes_info_SEEG{1,3}); str2num(electrodes_info_SEEG{1,4})] .* factor;
% other
ChannelMat.Channel(end).Orient = [];
ChannelMat.Channel(end).Weight = 1;
ChannelMat.Channel(end).Comment = [];
[tmp, iChannelStudy] = bst_get('ChannelForStudy', iStudy);
db_set_channel(iChannelStudy, ChannelMat, 2, 2);
% Load data :
data = readNPY( fullfile(EEG_folder, sprintf('%s_task-rest_run-01_epochs.npy', selectsubj{iSubject})));
dataSEEG = readNPY( fullfile(iEEG_folder, sprintf('%s_task-rest_run-01_epochs.npy', selectsubj{iSubject})));
ChannelFlag = ones(nChan+1,1);
ChannelFlag( strcmp(channel_info(:,7), 'bad')) = -1;
epochs_info = in_tsv(fullfile(EEG_folder, sprintf('%s_task-rest_run-01_epochs.tsv', selectsubj{iSubject})));
timeVector = linspace(-str2double(epochs_info{1,2}),str2double(epochs_info{1,2}), size(data,3));
for iEpoch = 1:size(data,1)
sDataOut = db_template('data');
tmp = zeros(nChan+1, length(timeVector));
tmp(1:size(data,2),:) = squeeze(data(iEpoch,:,:));
tmp(end,:) = squeeze(dataSEEG(iEpoch,:,:));
sDataOut.F = tmp;
sDataOut.Comment = sprintf('Epooch %d', iEpoch);
sDataOut.ChannelFlag = ChannelFlag;
sDataOut.Time = timeVector;
sDataOut.DataType = 'recordings';
sDataOut.nAvg = 1;
OutputFile = bst_process('GetNewFilename', bst_fileparts(sStudy.FileName), 'data_spikes');
sDataOut.FileName = file_short(OutputFile);
bst_save(OutputFile, sDataOut, 'v7');
% Register in database
db_add_data(iStudy, OutputFile, sDataOut);
end
end
The only issue is with the optodes coordinates as it seems brainstorm is not doing the co-registration as expected:
If I use the GUI to then import the coordinate; it is working (add electrodes position > EEG BIDS electrodes.tsv)
(note: actually; it seems they are not sharing the entire SEEG recording but only the data of one contact so less interesting ... still interesting to see if we can import it :))