Neurocognitive Dynamics of Translating Information From a Spatial Map Into Action.

1. clear bemobil_config
3. %% General Setup
5. % !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
6. % foldernames (NEED to have a filesep at the end, sorry!)
7. % !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
9. bemobil_config.filename_prefix = 'sub-';
11. % ------------ IMPORTANT --------------
12. % Adapt this data path to the place where you put the example data!
13. bemobil_config.study_folder = 'C:\Users\cleme\Desktop\iVTT\';
14. % ------------ IMPORTANT --------------
16. bemobil_config.source_data_folder = ['0_source-data' filesep];
17. bemobil_config.bids_data_folder = ['1_BIDS-data' filesep];
18. bemobil_config.raw_EEGLAB_data_folder = ['2_raw-EEGLAB' filesep];
19. bemobil_config.EEG_preprocessing_data_folder = ['3_EEG-preprocessing' filesep];
20. bemobil_config.spatial_filters_folder = ['4_spatial-filters' filesep];
21. bemobil_config.spatial_filters_folder_AMICA = ['4-1_AMICA' filesep];
22. bemobil_config.single_subject_analysis_folder = ['5_single-subject-EEG-analysis' filesep];
23. bemobil_config.motion_analysis_folder = ['6_single-subject-motion-analysis' filesep];
25. % filenames
26. bemobil_config.merged_filename = 'merged_EEG.set';
27. bemobil_config.basic_prepared_filename = 'basic_prepared.set';
28. bemobil_config.preprocessed_filename = 'preprocessed.set';
29. bemobil_config.filtered_filename = 'filtered.set';
30. bemobil_config.amica_filename_output = 'AMICA.set';
31. bemobil_config.dipfitted_filename = 'dipfitted.set';
32. bemobil_config.preprocessed_and_ICA_filename = 'preprocessed_and_ICA.set';
33. bemobil_config.single_subject_cleaned_ICA_filename = 'cleaned_with_ICA.set';
34. bemobil_config.merged_motion_filename = 'merged_MOTION.set';
35. bemobil_config.processed_motion_filename = 'motion_processed.set';
37. %% Preprocessing
39. % enter channels that you did not use at all (e.g. with our custom MoBI 160 chan layout, only 157 chans are used), leave
40. % empty, if all channels are used
41. % process_config.channels_to_remove = {'N29' 'N30' 'N31'};
42. bemobil_config.channels_to_remove = [];
44. % enter EOG channel names here:
45. % bemobil_config.eog_channels = {'VEOG', 'HEOG'};
46. bemobil_config.eog_channels = {'EOG'};
48. % if you add a channel here it needs to have a location as well. this means a new channel will be created and the old
49. % reference will be back in the dataset. if you don't know or don't need the reference, leave this empty
50. %bemobil_config.ref_channel = 'CPz';
51. bemobil_config.ref_channel = [];
53. % If all channels have a prefix it can be removed here, by entering a single char in the cell array. it's also possible
54. % to rename single channels here if needed. for this, enter a matrix of channel names (nbchans,2 (from->to))
55. bemobil_config.rename_channels = {};
57. % resample frequency during preprocessing (leave empty if you resample before, or your data is already correctly
58. % sampled)
59. bemobil_config.resample_freq = 250;
60. % bemobil_config.resample_freq = [];
62. % automatic channel cleaning:
63. % chancorr_crit - Correlation threshold. If a channel is correlated at less than this value
64. % to its robust estimate (based on other channels), it is considered abnormal in
65. % the given time window. OPTIONAL, default = 0.8.
66. % chan_max_broken_time - Maximum time (either in seconds or as fraction of the recording) during which a
67. % retained channel may be broken. Reasonable range: 0.1 (very aggressive) to 0.6
68. % (very lax). OPTIONAL, default = 0.5.
69. % chan_detect_num_iter - Number of iterations the bad channel detection should run (default = 10)
70. % chan_detected_fraction_threshold - Fraction how often a channel has to be detected to be rejected in the final
71. % rejection (default 0.5)
72. % flatline_crit - Maximum duration a channel can be flat in seconds (default 'off')
73. % line_noise_crit - If a channel has more line noise relative to its signal than this value, in
74. % standard deviations based on the total channel population, it is considered
75. % abnormal. (default: 'off')
76. % num_chan_rej_max_target - Target max amount of channel rejection. Actual num of rejections might be higher if
77. % there are a lot of bad channels. Target precision can be increased with higher chan_detect_num_iter
78. % If empty, use only chan_detected_fraction_threshold. Can be either a fraction
79. % of all channels (will be rounded, e.g. 1/5 of chans) or a specific integer number
81. bemobil_config.chancorr_crit = 0.8;
82. bemobil_config.chan_max_broken_time = 0.5;
83. bemobil_config.chan_detect_num_iter = 20;
84. bemobil_config.chan_detected_fraction_threshold = 0.5;
85. bemobil_config.flatline_crit = 'off';
86. bemobil_config.line_noise_crit = 'off';
87. bemobil_config.num_chan_rej_max_target = 1/5;
89. % channel locations: leave this empty if you have standard channel names that should use standard 10-20 locations,
90. % otherwise every dataset needs to have a channel locations file in the raw_data folder, and the chanloc file needs to
91. % have the correct participant prefix!
93. bemobil_config.channel_locations_filename = 'Location.ced';
94. %bemobil_config.channel_locations_filename = [];
96. % ZapLine-Plus to reduce line noise frequencies. Automatically finds noise frequencies and removes them as good as
97. % possible with Zapline. See 'help clean_data_with_zapline_plus' for more info about parameter tweaking.
99. % If the 'noisefreqs' field is set to empty, searches automatically, but you can also enter predefined noise frequencies
100. % here as a vector.
102. % Set the whole 'bemobil_config.zaplineConfig' field to [] if no noise is present in your data (haha).
104. bemobil_config.zaplineConfig.noisefreqs = [];
105. %% AMICA Parameters
107. % filter for AMICA:
108. % See Klug & Gramann (2020) for an investigation of filter effect on AMICA -> 1.25 Hz should be a good compromise if you
109. % don't know how much movement exists, otherwise even higher may be good, up to 2Hz, and you need to subtract 0.25 to
110. % obtain the correct cutoff value for a filter order of 1650
111. bemobil_config.filter_lowCutoffFreqAMICA = 1.75; % 1.75 is 1.5Hz cutoff!
112. bemobil_config.filter_AMICA_highPassOrder = 1650; % was used by Klug & Gramann (2020)
113. bemobil_config.filter_highCutoffFreqAMICA = []; % not used
114. bemobil_config.filter_AMICA_lowPassOrder = [];
116. % additional AMICA settings
117. bemobil_config.num_models = 1; % default 1
118. bemobil_config.AMICA_autoreject = 1; % uses automatic rejection method of AMICA. no time-cleaning (manual or automatic) is needed then!
119. bemobil_config.AMICA_n_rej = 20; % default 10
120. bemobil_config.AMICA_reject_sigma_threshold = 3; % default 3
121. bemobil_config.AMICA_max_iter = 2000; % default 2000
123. % on some PCs AMICA may crash before the first iteration if the number of threads and the amount the data does not suit
124. % the algorithm. Jason Palmer has been informed, but no fix so far. just roll with it. if you see the first iteration
125. % working there won't be any further crashes. in this case just press "close program" or the like and the
126. % bemobil_spatial_filter algorithm will AUTOMATICALLY reduce the number of threads and start AMICA again. this way you
127. % will always have the maximum number of threads that should be used for AMICA. check in the task manager how many
128. % threads you have theoretically available and think how much computing power you want to devote for AMICA.
130. % 4 threads are most effective for single subject speed, more threads don't really shorten the calculation time much.
131. % best efficiency is using just 1 thread and have as many matlab instances open as possible (limited by the CPU usage).
132. % Remember your RAM limit in this case.
134. bemobil_config.max_threads = 4; % default 4
136. % for warping the electrode locations to the standard 10-20 locations (leave
137. % empty if using standard locations)
138. % bemobil_config.warping_channel_names = {3,'FTT9h';45,'FTT10h';84,'AFz';87,'Cz'};
139. bemobil_config.warping_channel_names = [];
141. % dipfit settings
142. bemobil_config.residualVariance_threshold = 100;
143. bemobil_config.do_remove_outside_head = 'off';
144. bemobil_config.number_of_dipoles = 1;
146. % IC_label settings
147. % 'default' classifier did not lead to good classification of muscles (see Klug & Gramann (2020)), 'lite' was better
148. % overall.
149. bemobil_config.iclabel_classifier = 'lite';
151. % 'Brain', 'Muscle', 'Eye', 'Heart', 'Line Noise', 'Channel Noise', 'Other'
152. bemobil_config.iclabel_classes = [1,7];
154. % if the threshold is set to -1, the popularity classifier is used (i.e. every IC gets the class with the highest
155. % probability), if it is set to a value, the summed score of the iclabel_classes must be higher than this threshold to
156. % keep an IC. Must be in the [0 1] range!
157. bemobil_config.iclabel_threshold = -1;
159. %% finalization
161. % filtering the final dataset
162. bemobil_config.final_filter_lower_edge = 0.3; % this should not lead to any issues downstream but remove all very slow drifts
163. bemobil_config.final_filter_higher_edge = 80;
165. %% Motion Processing Parameters
167. bemobil_config.lowpass_motion = 8;
168. bemobil_config.lowpass_motion_after_derivative = 24;
170. try
171. pop_editoptions('option_saveversion6', 0, 'option_single', 0, 'option_memmapdata', 0, 'option_savetwofiles', 1, 'option_storedisk', 0);
172. catch
173. warning('Could NOT edit EEGLAB memory options!!');
174. end

Clement_bemobil_config_script_ivtt.m, no license · at the source