script automagic

src/automagic/janvier/script25janv.m

@@ -0,0 +1,54 @@
+%Parameter=load('/udd/nforde/Nina/StageEEGpre/data/RAWformat_Test4_results/project_state.mat')
+restoredefaultpath;
+clear all; 
+clc; %First, clean the environment
+
+addpath( '/home/nforde/Documents/StageEEGpre/dependencies/automagic-master');
+
+
+addAutomagicPaths();
+
+name = '24janv2';
+dataFolder = '/home/nforde/Documents/StageEEGpre/data/formatBIDS';
+resultsFolder = '/home/nforde/Documents/StageEEGpre/data/formatBIDS_24janv_results2';
+ext = '.dat';
+
+% Params= struct('FilterParams',         struct('high',  struct('freq',  0.1000, 'order', []),... % Default order for filtering
+%                                                'low',   struct('freq',  35, 'order', [])),...
+%                  'CRDParams',        struct([]),...
+%                  'PrepParams',          struct('lineFrequencies', 50), ...
+%                  'HighvarParams',       struct('sd', 25,...
+%                                                 'cutoff', 100, ...
+%                                                 'rejRatio', 0.5000), ...
+%                  'MinvarParams',       struct('sd', 1),...
+%                  'InterpolationParams', struct('method', 'spherical'), ...
+%                  'ICLabelParams',       struct([]),...
+%                 'EEGSystem',           struct('name', 'EGI',...
+%                                                'sys10_20', 0, ...
+%                                                'locFile', '', ...
+%                                                'refChan', struct('idx', []), ...
+%                                                'fileLocType', '',...
+%                                                'eogChans', [], ...
+%                                                'tobeExcludedChans', []), ...
+%                  'Settings',            struct('trackAllSteps', 1, ...
+%                                                'pathToSteps', '/allSteps.mat',...
+%                                                'colormap','Default',...
+%                                                'sortChans', 0)...
+%                  );
+
+Params=load('/home/nforde/Documents/StageEEGpre/data/formatBIDS_24janv_results2/project_state.mat');
+Params=Params.self.params;
+sRate= [];
+VisualisationParams = struct();
+
+
+
+
+
+% Template for all the parameters
+
+
+
+project = Project(name, dataFolder, resultsFolder, ext, Params, VisualisationParams,sRate);
+project.preprocessAll();
+%project.interpolateSelected();

src/automagic/janvier/segmentation.m

@@ -0,0 +1,37 @@
+%dd
+restoredefaultpath;
+clear all; 
+clc; 
+
+addpath(genpath('/home/nforde/Documents/StageEEGpre/dependencies/article/MATLAB-EEG-preProcessing-master'))% pour doSegment
+addpath(genpath('/home/nforde/Documents/StageEEGpre/dependencies/eeglab_current/eeglab2021.1'))% pour pop rmbase
+
+
+dataFolder = '/home/nforde/Documents/StageEEGpre/data/formatBIDS_24janv_results2/sujets2';
+cd(dataFolder)
+filenames = dir('allSteps_RewardProcessing*') %Compile list of all data
+
+
+for participant = 1:2%Cycle through participants
+
+    %Get participant name information
+    disp(['Participant: ', num2str(participant)]) %Display current participant being processed
+    participant_number = strsplit(filenames(participant).name(1:end-4),'_') %Split filename into components
+    participant_varname = ['segmented',participant_number{3}] %Create new file name
+    EEG = []; %Clear past data
+    file=load(filenames(participant).name); %Load participant output
+    EEG=file.EEGFinal
+
+
+
+
+     %Determine markers of interest for WAV later
+    markers = {'S110','S111'}; %Loss, win
+
+
+    [EEG] = doSegmentData(EEG,markers,[-500 1498]); %Segment Data (S110 = Loss, S111 = Win). The segment window of interest is -200 to 1000ms, and we here add 300 ms before and after this because time-frequency edge artifacts (this is different than the first pass because we were being more conservative then)
+    %baseline correction
+    EEG = pop_rmbase( EEG, [-200/1000,0]);
+    save(participant_varname,'EEG') %Save the current output
+
+end