preproc functions

LabNeuroCogDevel · Oct 28, 2024 · d622408 · d622408
1 parent a37995b
commit d622408
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Showing 5 changed files with 22 additions and 11 deletions.
diff --git a/.gitignore b/.gitignore
@@ -51,3 +51,4 @@ sEEG/
 choice-landscape/
 0c43526d20387f01a0f149d0888f1f5d27d85850
 preprocessed_data/
+Signal_Complexity/
diff --git a/Preprocessing_Functions/epochlean.m b/Preprocessing_Functions/epochlean.m
@@ -1,8 +1,9 @@
-function [revisar] = epochlean(inputfile,epoch_folder,epoch_rj_marked_folder)
+function [revisar] = epochlean(inputfile,epoch_folder,epoch_rj_marked_folder,task,taskdirectory)
 revisar = {};
 % what file are we using
 
-locs = file_locs(inputfile);
+% locs = file_locs(inputfile,epoch_folder,task);
+locs = file_locs(inputfile,taskdirectory,task);
 if exist(locs.epochClean, 'file')
     OUTEEG = [];
     fprintf('skipping; already created %s\n', locs.epochClean);
@@ -34,7 +35,15 @@
 
 %% epoching: -0.500 to 2 seconds
 %extract epochs
-EEG = pop_epoch( EEG, {'-5' '-3' '0' '1' '2' '3' '4' '5'}, [-0.5  2], 'newname', [currentName '_epochs'], 'epochinfo', 'yes');
+if task == "MGS"
+    EEG = pop_epoch( EEG, {'-5' '-3' '0' '1' '2' '3' '4' '5'}, [-0.5  2], 'newname', [currentName '_epochs'], 'epochinfo', 'yes');
+
+elseif task == "anti"
+
+    EEG = pop_epoch( EEG, {'1' '2' '3'}, [0  0.5], 'newname', [currentName '_epochs'], 'epochinfo', 'yes');
+
+
+end
 
 % %remove baseline
 % EEG = pop_rmbase( EEG, [-400    0]);

diff --git a/Preprocessing_Functions/preprocessing_pipeline.m b/Preprocessing_Functions/preprocessing_pipeline.m
@@ -209,7 +209,7 @@
 else
     [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
 
-    if ~any(find(cellfun (@any,regexpi (fieldnames(EEG.etc), 'clean_channel_mask'))));
+    if ~any(find(cellfun (@any,regexpi (fieldnames(EEG.etc), 'clean_channel_mask'))))
         EEG.etc.clean_channel_mask=42;
     else
     end

diff --git a/Preprocessing_Functions/runICAs.m b/Preprocessing_Functions/runICAs.m
@@ -96,7 +96,6 @@
 % fprintf('saving %s\n', fullfile(outpath, [name '_SAS.set']))
 % EEG = pop_saveset( EEG, 'filename',[name,'_SAS.set'], 'filepath', outpath); %save final preprocessed output
 
-
 EEG = pop_runica(EEG, 'extended',1,'interupt','on','PCA',30); 
 
 %create file name

diff --git a/Preprocessing_Functions/run_preprocessing_pipeline.m b/Preprocessing_Functions/run_preprocessing_pipeline.m
@@ -3,9 +3,11 @@
 % load in paths to feildtrip and eeglab 
 addpath(genpath('/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/Preprocessing_Functions/'));
 addpath(genpath('/resources/Euge/'))
+addpath('/Volumes/Hera/Projects/7TBrainMech/scripts/fieldtrip-20220104/')
 % run('/Volumes/Hera/Projects/7TBrainMech/scripts/eeg/Shane/resources/eeglab2022.1/eeglab.m');
 run('/Volumes/Hera/Abby/Resources/eeglab_current/eeglab2024.2/eeglab.m')
 
+
 % Outpath
 % maindir = hera('Projects/7TBrainMech/scripts/eeg/Shane/preprocessed_data');
 maindir = hera('Abby/preprocessed_data');
@@ -101,20 +103,20 @@
 end
 
 
-if task == "MGS"
+if task == "MGS" || task == "anti"
     %% Clean epochs to remove
-
-    epoch_path = [outpath '/AfterWhole/ICAwholeClean/'];
-    epoch_folder = [outpath '/AfterWhole/epoch/'];
-    epoch_rj_marked_folder = [outpath '/AfterWhole/epochclean/'];
+    path_data = [taskdirectory '/AfterWhole/ICAwholeClean/'];
+    epoch_path = [taskdirectory '/AfterWhole/ICAwholeClean/'];
+    epoch_folder = [taskdirectory '/AfterWhole/epoch/'];
+    epoch_rj_marked_folder = [taskdirectory '/AfterWhole/epochclean/'];
 
     EEGfileNames = dir([path_data, '/*_icapru.set']);
 
     revisar = {};
     for currentEEG = 1:size(EEGfileNames,1)
         filename = [EEGfileNames(currentEEG).name];
         inputfile = [epoch_path,filename];
-        revisar{currentEEG} = epochlean(inputfile,epoch_folder,epoch_rj_marked_folder);
+        revisar{currentEEG} = epochlean(inputfile,epoch_folder,epoch_rj_marked_folder,task,taskdirectory);
     end
 end