-
Notifications
You must be signed in to change notification settings - Fork 20
/
template_bemobil_import.m
220 lines (180 loc) · 13.9 KB
/
template_bemobil_import.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
% initialize EEGLAB
if ~exist('ALLCOM','var')
eeglab;
end
% initialize fieldtrip without adding alternative files to path
% assuming FT is on your path already or is added via EEGlab plugin manager
global ft_default
ft_default.toolbox.signal = 'matlab'; % can be 'compat' or 'matlab'
ft_default.toolbox.stats = 'matlab';
ft_default.toolbox.image = 'matlab';
ft_defaults % this sets up the FieldTrip path
%% [OPTIONAL] check the .xdf data to explore the structure
ftPath = fileparts(which('ft_defaults'));
addpath(fullfile(ftPath, 'external','xdf'));
xdfPath = '...yourpath\yourfile.xdf'; % enter full path to your .xdf file
% load .xdf data to check what is in there
streams = load_xdf(xdfPath);
streamnames = cellfun(@(x) x.info.name, streams, 'UniformOutput', 0)' % will display names of streams contained in .xdf
% display names of all channels in the .xdf data
for Si = 1:numel(streamnames)
if isfield( streams{Si}.info.desc, 'channels')
channelnames = cellfun(@(x) x.label, streams{Si}.info.desc.channels.channel, 'UniformOutput', 0)'
end
end
%% [OPTIONAL] enter metadata about the data set, data modalities, and participants
% general metadata shared across all modalities
% will be saved in BIDS-folder/data_description.json
% see "https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#:~:text=LICENSE-,dataset_description.json,-The%20file%20dataset_description"
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
generalInfo = [];
% required for dataset_description.json
generalInfo.dataset_description.Name = 'name of your data set';
generalInfo.dataset_description.BIDSVersion = 'version of BIDS-specification you are following'; % if sharing motion data, use "unofficial extension"
% optional for dataset_description.json
generalInfo.dataset_description.License = 'licence type';
generalInfo.dataset_description.Authors = {"author 1", "author 2", "author 3"};
generalInfo.dataset_description.Acknowledgements = 'acknowledgement text';
generalInfo.dataset_description.Funding = {"funding source 1", "funding source 2"};
generalInfo.dataset_description.ReferencesAndLinks = {"reference", "link to article"};
generalInfo.dataset_description.DatasetDOI = 'DOI of your data set';
% general information shared across modality specific json files
generalInfo.InstitutionName = 'name of your institute';
generalInfo.InstitutionalDepartmentName = 'name of your department';
generalInfo.InstitutionAddress = 'address of your institute';
generalInfo.TaskDescription = 'text describing your task';
% information about the eeg recording system
% will be saved in BIDS-folder/sub-XX/[ses-XX]/eeg/*_eeg.json and *_coordsystem.json
% see "https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/03-electroencephalography.html#:~:text=MAY%20be%20specified.-,Sidecar%20JSON%20(*_eeg.json),-Generic%20fields%20MUST"
% and "https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/03-electroencephalography.html#:~:text=after%20the%20recording.-,Coordinate%20System%20JSON,-(*_coordsystem.json"
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
eegInfo = [];
eegInfo.coordsystem.EEGCoordinateSystem = 'enter the name of your coordinate system'; % only needed when you share eloc
eegInfo.coordsystem.EEGCoordinateUnits = 'enter the unit of your coordinate system'; % only needed when you share eloc
eegInfo.coordsystem.EEGCoordinateSystemDescription = 'enter description of your coordinate system'; % only needed when you share eloc
eegInfo.eeg.SamplingFrequency = 1000; % nominal sampling frequency
% information about the motion recording system
% will be saved in BIDS-folder/sub-XX/[ses-XX]/motion/*_motion.json
% see "https://docs.google.com/document/d/1iaaLKgWjK5pcISD1MVxHKexB3PZWfE2aAC5HF_pCZWo/edit?usp=sharing"
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
motionInfo = [];
tracking_systems = {'System1', 'System2'}; % enter the names of your tracking systems
% motion specific fields in json
motionInfo.motion = [];
% system 1 information
motionInfo.motion.TrackingSystems(1).TrackingSystemName = tracking_systems{1};
motionInfo.motion.TrackingSystems(1).Manufacturer = 'HTC'; % manufacturer of the motion capture system
motionInfo.motion.TrackingSystems(1).ManufacturersModelName = 'Vive Pro'; % model name of the tracking system
motionInfo.motion.TrackingSystems(1).SamplingFrequency = 90; % If no nominal Fs exists, n/a entry returns 'n/a'. If it exists, n/a entry returns nominal Fs from motion stream.
motionInfo.motion.TrackingSystems(1).DeviceSerialNumber = 'n/a';
motionInfo.motion.TrackingSystems(1).SoftwareVersions = 'n/a';
motionInfo.motion.TrackingSystems(1).SpatialAxes = 'FRU'; % XYZ spatial axes description
motionInfo.motion.TrackingSystems(1).RotationRule = 'left-hand'; % if rotation is present, does it follow the left-hand or right-hand rule?
motionInfo.motion.TrackingSystems(1).RotationOrder = 'ZXY'; % order of euler angles' extrinsic rotation
% system 2 information
motionInfo.motion.TrackingSystems(2).TrackingSystemName = tracking_systems{2};
motionInfo.motion.TrackingSystems(2).Manufacturer = 'Impuls X2';
motionInfo.motion.TrackingSystems(2).ManufacturersModelName = 'PhaseSpace';
motionInfo.motion.TrackingSystems(2).SamplingFrequency = 90;
motionInfo.motion.TrackingSystems(2).DeviceSerialNumber = 'n/a';
motionInfo.motion.TrackingSystems(2).SoftwareVersions = 'n/a';
motionInfo.motion.TrackingSystems(2).SpatialAxes = 'FRU';
motionInfo.motion.TrackingSystems(2).RotationRule = 'left-hand';
motionInfo.motion.TrackingSystems(2).RotationOrder = 'ZXY';
% participant information
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
% here describe the fields in the participant file
% see "https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file:~:text=UTF%2D8%20encoding.-,Participants%20file,-Template%3A"
% for numerical values :
% subjectData.fields.[insert your field name here].Description = 'describe what the field contains';
% subjectData.fields.[insert your field name here].Unit = 'write the unit of the quantity';
% for values with discrete levels :
% subjectData.fields.[insert your field name here].Description = 'describe what the field contains';
% subjectData.fields.[insert your field name here].Levels.[insert the name of the first level] = 'describe what the level means';
% subjectData.fields.[insert your field name here].Levels.[insert the name of the Nth level] = 'describe what the level means';
%--------------------------------------------------------------------------
subjectInfo.fields.nr.Description = 'numerical ID of the participant';
subjectInfo.fields.age.Description = 'age of the participant';
subjectInfo.fields.age.Unit = 'years';
subjectInfo.fields.sex.Description = 'sex of the participant';
subjectInfo.fields.sex.Levels.M = 'male';
subjectInfo.fields.sex.Levels.F = 'female';
subjectInfo.fields.handedness.Description = 'handedness of the participant';
subjectInfo.fields.handedness.Levels.R = 'right-handed';
subjectInfo.fields.handedness.Levels.L = 'left-handed';
% names of the columns - 'nr' column is just the numerical IDs of subjects
% do not change the name of this column
subjectInfo.cols = {'nr', 'age', 'sex', 'handedness'};
subjectInfo.data = {1, 30, 'F', 'R' ; ...
2, 22, 'M', 'R'; ...
3, 23, 'F', 'R'; ...
4, 34, 'M', 'R'; ...
5, 25, 'F', 'R'; ...
6, 21, 'F', 'R' ; ...
7, 28, 'M', 'R'; ...
8, 28, 'M', 'R'; ...
9, 24, 'F', 'R'; ...
10, 25, 'F', 'L'; ...
11, 30, 'F', 'R'; ...
12, 22, 'M', 'R'; ...
13, 23, 'F', 'R'; ...
14, 34, 'M', 'R'; ...
15, 25, 'F', 'R'; ...
16, 21, 'F', 'R' ; ...
17, 28, 'M', 'R'; ...
18, 28, 'M', 'R'; ...
19, 24, 'F', 'R'; ...
20, 25, 'F', 'L';};
%% iterate over participants, sessions, and runs to import file-by-file
studyFolder = '...\yourstudyfolder'; % full path to your study folder
sessionNames = {'sessionA', 'ssssionB'}; % replace with names of your sessions (if there are no multiple sessions, remove confg.ses and the session loop in the following)
% loop over participants
for subject = 1:20
% loop over sessions
for session = 1:2
config = []; % reset for each loop ´
config.bids_target_folder = '...\BIDS-data'; % required, replace with the folder where you want to store your bids data
config.filename = fullfile('...\yourxdffile.xdf'); % required, replace with your xdf file full path
config.eeg.chanloc = fullfile('...\yourelocfile.elc'); % optional, if you have electrode location file, replace with the full patht to the file.
config.task = 'YourTaskName'; % optional, replace with your task name
config.subject = subject; % required
config.session = sessionNames{session}; % optional
config.overwrite = 'on'; % optional
config.eeg.stream_name = 'YourEEGStreamName'; % required, replace with the unique keyword in your eeg stream in the .xdf file
%------------------------------------------------------------------
config.motion.streams{1}.xdfname = 'YourStreamNameInXDF'; % replace with name of the stream corresponding to the first tracking system
config.motion.streams{1}.bidsname = tracking_systems{1}; % a comprehensible name to represent the tracking system
config.motion.streams{1}.tracked_points = 'headRigid'; % name of the point that is being tracked in the tracking system, the keyword has to be containted in the channel name (see "bemobil_bids_motionconvert")
config.motion.streams{1}.tracked_points_anat= 'head'; % example of how the tracked point can be renamed to body part name for metadata
% names of position and quaternion channels in each stream
config.motion.streams{1}.positions.channel_names = {'headRigid_Rigid_headRigid_X'; 'headRigid_Rigid_headRigid_Y' ; 'headRigid_Rigid_headRigid_Z' };
config.motion.streams{1}.quaternions.channel_names = {'headRigid_Rigid_headRigid_quat_W';'headRigid_Rigid_headRigid_quat_Z';...
'headRigid_Rigid_headRigid_quat_X';'headRigid_Rigid_headRigid_quat_Y'};
config.motion.streams{2}.xdfname = 'YourStreamNameInXDF2';
config.motion.streams{2}.bidsname = tracking_systems{2};
config.motion.streams{2}.tracked_points = {'Rigid1', 'Rigid2', 'Rigid3', 'Rigid4'}; % example when there are multiple points tracked by the system
config.motion.streams{2}.positions.channel_names = {'Rigid1_X', 'Rigid2_X', 'Rigid3_X', 'Rigid4_X';... % each column is one tracked point and rows are different coordinates
'Rigid1_Y', 'Rigid2_Y', 'Rigid3_Y', 'Rigid4_Y';...
'Rigid1_Z', 'Rigid2_Z', 'Rigid3_Z', 'Rigid4_Z'};
config.motion.streams{2}.quaternions.channel_names = {'Rigid1_A', 'Rigid2_A', 'Rigid3_A', 'Rigid4_A';...
'Rigid1_B', 'Rigid2_B', 'Rigid3_B', 'Rigid4_B';...
'Rigid1_C', 'Rigid2_C', 'Rigid3_C', 'Rigid4_C'; ...
'Rigid1_D', 'Rigid2_D', 'Rigid3_D', 'Rigid4_D'};
bemobil_xdf2bids(config, ...
'general_metadata', generalInfo,...
'participant_metadata', subjectInfo,...
'motion_metadata', motionInfo, ...
'eeg_metadata', eegInfo);
end
fclose all
%% configuration for bemobil bids2set
%----------------------------------------------------------------------
config.set_folder = fullfile(studyFolder,'2_raw-EEGLAB');
config.session_names = sessionNames;
config.other_data_types = {'motion'}; % specify which other data type than eeg is there (only 'motion' and 'physio' supported atm)
bemobil_bids2set(config);
end