add sub 10

data_curration/bidsify.m

@@ -1,6 +1,6 @@
 clear; clc;
 
-subs = [1:7 12];
+subs = [1:7 10 12];
 
 overwrite_cfg = [];
 overwrite_cfg.anat = false;

data_curration/pilot_convert_raw1_to_raw2.m

@@ -0,0 +1,224 @@
+%% Add util dir to path
+addpath('/project/3031004.01/meg-ahat/util')
+
+%% Set pilot data directory
+raw2_dir = '/project/3031004.01/pilot-data/raw2';
+raw1_dir = '/project/3031004.01/pilot-data/raw1';
+%%
+copyfile (raw1_dir, raw2_dir);
+
+%% Set up logging
+diaryfile = strcat(raw2_dir, '/raw1_to_raw2.log');
+diary (diaryfile)
+
+%% Setup Fieldtrip
+configure_ft
+
+% Sebject (defined as cell array for future compatibility)
+subj = {
+  '099'
+  };
+
+ses = 1;
+runindx = 1;
+
+% Tasks in the two runs
+tasks = {
+  'visualattention';
+  'workingmemory'
+};
+
+dataset_dir = sprintf('%s/sub-%s/ses-00%d/meg/sub-%s_ses-00%d_task-flicker_meg.ds', raw2_dir, subj{1}, ses, subj{1}, ses);
+cfg = [];
+cfg.dataset = dataset_dir;
+
+%%
+% read the header information and the events from the meg data
+hdr   = ft_read_header(cfg.dataset);
+event = ft_read_event(cfg.dataset);
+
+% search for "trigger" events
+mask = find(strcmp('UPPT001', {event.type}));
+value  = [event(mask).value]';
+mask_start_events = find(value == 1);
+timestamp = [event(mask).timestamp]';
+sample = [event(mask).sample]';
+
+% look for the combination of a trigger "5" followed by a trigger "6"
+% for each trigger except the last one
+sample_list = [];
+onset_list = [];
+duration_list = [];
+rt_list = [];
+for j = 1:(length(value)-1)
+    if not(j>1)
+        continue
+    end
+
+    trg1 = value(j-1);
+    trg2 = value(j);
+
+    if trg1==4 && trg2==5
+      trlbegin = sample(j);
+      onset = timestamp(j);
+
+      % Look ahead for the "rest" trigger (2) or final trigger (8)
+      for i = 1:20
+          try
+            trg3 = value(j+i);
+            if trg3==2 || trg3==8
+                end_index = j + i;
+                break
+            end
+          catch ME
+            if (strcmp(ME.identifier, 'MATLAB:badsubscript'))
+                end_index = j + i - 1;
+                break
+            end
+          end
+      end
+
+      % find response and calculate rt
+      try
+          trg4 = value(j+1);
+          trg5 = value(j+2);
+      catch ME
+          if (strcmp(ME.identifier, 'MATLAB:badsubscript'))
+            break
+          end
+      end
+      if trg4==6 % discrimination grating
+        rt = -1;
+        if trg5==7 % response given
+            rt = timestamp(j+2) - timestamp(j+1);
+        end
+      else % catch trial
+        rt = -2;
+      end
+
+      duration = timestamp(end_index) - onset;
+
+      sample_list = [sample_list; trlbegin];
+      onset_list = [onset_list; onset];
+      duration_list = [duration_list; duration];
+      rt_list = [rt_list; rt];
+    end
+end
+
+%% Load behavioural data events
+% Specify source path
+beh_dir = sprintf('%s/sub-%s/ses-00%d/beh/', raw2_dir, subj{1}, ses);
+filename = sprintf('sub-%s_ses-00%d_run-00%d_task-%s_events.tsv', subj{1}, ses, runindx, tasks{runindx});
+d = dir(strcat(beh_dir, filename));
+% Load the behavioural data as a table
+beh_log = readtable(fullfile(d.folder, d.name), "FileType","text",'Delimiter', '\t');
+beh_log.rt_meg = repmat(-3, size(beh_log, 1), 1);
+beh_log.sample = repmat(-1, size(beh_log, 1), 1);
+% reorder columns
+beh_log = beh_log(:, [1:2 end 3:end-1]);
+
+beh_log.onset = onset_list(1:height(beh_log));
+beh_log.duration = duration_list(1:height(beh_log));
+beh_log.sample = sample_list(1:height(beh_log));
+beh_log.rt_meg = rt_list(1:height(beh_log));
+
+% Save updated table
+writetable(beh_log, fullfile(d.folder, d.name), 'filetype','text', 'delimiter','\t')
+
+%% Iterate over MEG _events.tsv and enrich with BEH info
+
+meg_events_fname = sprintf('%s/sub-%s/ses-00%d/meg/sub-%s_ses-00%d_task-flicker_events.tsv', raw2_dir, subj{1}, ses, subj{1}, ses);
+meg_events = readtable(meg_events_fname, "FileType","text",'Delimiter', '\t');
+
+meg_events.trial_number = repmat("n/a", height(meg_events), 1);
+meg_events.block_number = repmat("n/a", height(meg_events), 1);
+meg_events.stimulus_condition = repmat("n/a", height(meg_events), 1);
+meg_events.task = repmat("n/a", height(meg_events), 1);
+meg_events.task_congruence = repmat("n/a", height(meg_events), 1);
+meg_events.response = repmat("n/a", height(meg_events), 1);
+meg_events.reaction_time = repmat(-3, height(meg_events), 1);
+meg_events.rt_meg = repmat(-3, height(meg_events), 1);
+
+
+meg_iterator = 0;
+beh_iterator = 1;
+while beh_iterator <= height(beh_log)
+    meg_iterator = meg_iterator + 1;
+
+    if not(meg_events.type(meg_iterator) == "UPPT001")
+        continue
+    end
+
+    beh_sample = beh_log.sample(beh_iterator);
+    meg_sample = meg_events.sample(meg_iterator);
+
+    if (beh_sample == meg_sample)
+        meg_events.trial_number(meg_iterator) = beh_log.trial_number(beh_iterator);
+        meg_events.block_number(meg_iterator) = beh_log.block_number(beh_iterator);
+        meg_events.stimulus_condition(meg_iterator) = beh_log.stimulus_condition(beh_iterator);
+        meg_events.task(meg_iterator) = beh_log.task(beh_iterator);
+        meg_events.task_congruence(meg_iterator) = beh_log.task_congruence(beh_iterator);
+        meg_events.response(meg_iterator) = beh_log.response(beh_iterator);
+        meg_events.reaction_time(meg_iterator) = beh_log.reaction_time(beh_iterator);
+        meg_events.rt_meg(meg_iterator) = beh_log.rt_meg(beh_iterator);
+        meg_events.duration{meg_iterator} = beh_log.duration(beh_iterator);
+
+        beh_iterator = beh_iterator + 1;
+    end
+
+end
+
+%meg_events.trial_number = cell2mat(meg_events.trial_number);
+%meg_events.block_number = cell2mat(meg_events.block_number);
+%meg_events.stimulus_condition = cell2mat(meg_events.stimulus_condition);
+%meg_events.task = cell2mat(meg_events.task);
+%meg_events.task_congruence = cell2mat(meg_events.task_congruence);
+%meg_events.response = cell2mat(meg_events.response);
+%meg_events.reaction_time = cell2mat(meg_events.reaction_time);
+%meg_events.rt_meg = cell2mat(meg_events.rt_meg);
+%meg_events.duration = cell2mat(meg_events.duration);
+
+% Save updated table
+meg_events_fname = sprintf('%s/sub-%s/ses-00%d/meg/sub-%s_ses-00%d_task-flicker_events.tsv', raw2_dir, subj{1}, ses, subj{1}, ses);
+writetable(meg_events, meg_events_fname, 'filetype','text', 'delimiter','\t')
+
+
+%% Add BIDS required columns to behavioural
+%log_len = size(log, 1);
+%log.onset = repmat("n/a", log_len, 1);
+%log.duration = repmat("n/a", log_len, 1);
+%log = log(:, [end-1:end 1:end-3]);
+
+% Specify the output path in the raw1 directory
+%filename = sprintf('sub-%s_ses-00%d_run-00%d_task-%s_events', subj{1}, sesindx, runindx, tasks{runindx});
+%out_file = strcat(filename, '.tsv');
+%out_d = fullfile(strcat(beh_dir, out_file));
+% Write the behavioural data to destination
+%writetable(log,out_d, 'filetype','text', 'delimiter','\t')
+
+
+%%
+
+diary off
+
+%%
+%cfg.trialfun = 'definetrial_va';
+%cfg.trialdef.pre  = 0.5;
+%cfg.trialdef.post =1;
+%cfg.continuous = 'yes';
+%cfg = ft_definetrial(cfg);%
+
+%%
+%cfg.demean = 'yes';
+%cfg.channel = 'meggrad';
+%data_meg = ft_preprocessing(cfg);
+%%
+%cfg          = [];
+%cfg.method   = 'trial';
+% cfg.ylim     = [-1e-12 1e-12];
+%dummy        = ft_rejectvisual(cfg, data_meg);
+
+%%
+%cfg = [];
+%cfg.continuous = 'yes';
+%artf = ft_databrowser(cfg, data_meg);