Merge pull request #140 from CCC-members/develop

Develop
CCC-members · Apr 14, 2024 · 96cb734 · 96cb734
2 parents d8d39b6 + c528f24
commit 96cb734
Show file tree

Hide file tree

Showing 3 changed files with 43 additions and 14 deletions.
diff --git a/functions/cfs_process_interface.m b/functions/cfs_process_interface.m
@@ -165,8 +165,7 @@
     disp("--------------------------------------------------------------------------");
     disp("CFS -->> Process Export subject");
     disp("--------------------------------------------------------------------------");
-    CiftiStorm      = process_integration(CiftiStorm, properties, subID, CSurfaces, sub_to_FSAve);
-    if(isequal(CiftiStorm.Participants(end).Status,'Rejected'));continue;end
+    CiftiStorm      = process_integration(CiftiStorm, properties, subID, CSurfaces, sub_to_FSAve);   
 
     disp(strcat('CFS -->> Subject:' , subID, '. Processing finished.'));
     disp('==========================================================================');    

diff --git a/functions/export/save_output_files.m b/functions/export/save_output_files.m
@@ -9,15 +9,18 @@
 end
 % Creating subject folder structure
 disp(strcat("-->> Creating subject output structure"));
-action                                  = 'all';
+if(~exist('action', 'var'))
+    action                              = 'all';
+end
 disp(strcat("-->> Creating subject output structure"));
-action = 'all';
 [output_subject_dir]                    = create_data_structure(base_path,subID,action);
 subject_info                            = struct;
 subject_info.name                       = subID;
-for i=1:length(MEEGs)
-    MEEG = MEEGs(i);
-    subject_info.meeg_dir{i}            = replace(fullfile('meeg',strcat(MEEG.filename,'.mat')),'\','/');
+if(isequal(action,'all'))
+    for i=1:length(MEEGs)
+        MEEG = MEEGs(i);
+        subject_info.meeg_dir{i}        = replace(fullfile('meeg',strcat(MEEG.filename,'.mat')),'\','/');
+    end
 end
 subject_info.leadfield_dir.leadfield    = replace(fullfile('leadfield','leadfield.mat'),'\','/');
 subject_info.leadfield_dir.AQCI         = replace(fullfile('leadfield','AQCI.mat'),'\','/');
@@ -29,10 +32,12 @@
 subject_info.completed                  = true;
 
 % Saving subject files
-disp ("-->> Saving MEEG file");
-for i=1:length(MEEGs)
-    EEG = MEEGs(i).EEG;
-    save(fullfile(output_subject_dir,subject_info.meeg_dir{i}),'-struct','EEG');
+if(isequal(action,'all'))
+    disp ("-->> Saving MEEG file");
+    for i=1:length(MEEGs)
+        EEG = MEEGs(i).EEG;
+        save(fullfile(output_subject_dir,subject_info.meeg_dir{i}),'-struct','EEG');
+    end
 end
 disp ("-->> Saving channel file");
 save(fullfile(output_subject_dir,subject_info.channel_dir),'-struct','Cdata');

diff --git a/functions/processes/process_integration.m b/functions/processes/process_integration.m
@@ -54,14 +54,39 @@
     EEG_path                    = fullfile(eeglab_path,subID);
     [MEEGs, HeadModels, Cdata]  = StructFunct_integration(EEG_path, modality, HeadModels, Cdata);
     AQCI                        = AutomaticQCI(HeadModels.HeadModel.Gain, Cdata, Scortex.Sc);
-    save_output_files(base_path, modality, subID, MEEGs, HeadModels, Cdata, Shead, Sout, Sinn, Scortex, AQCI);
+    if(isempty(fields(MEEGs)))
+        action = 'anat';  
+        CiftiStorm.Participants(end).Status             = "Structural";
+    else
+        action = 'all';
+        CiftiStorm.Participants(end).Status             = "Completed";
+    end
+    save_output_files(base_path, modality, subID, MEEGs, HeadModels, Cdata, Shead, Sout, Sinn, Scortex, AQCI, action);    
+    CiftiStorm.Participants(end).FileInfo               = strcat(subID,".json");
+    CiftiStorm.Participants(end).Process(end+1).Name    = "Integration";
+    CiftiStorm.Participants(end).Process(end).Status    = "Completed";
+    CiftiStorm.Participants(end).Process(end).Error     = [];
 else
     CiftiStorm.Template = CiftiStorm.Participants;
+    disp(strcat("-->> Saving anatomy template: ",template_name));
+    disp("--------------------------------------------------------------------------");
+    CiftiStorm.Template.SubID       = template_name;
+    CiftiStorm.Template.Status      = "Anatomy";
+    CiftiStorm.Template.FileInfo    = strcat(template_name,'.json');
+    subID                           = template_name;
+    HeadModels                      = rawHeadModels;
+    Cdata                           = rawCdata;
+    AQCI                            = AutomaticQCI(HeadModels.HeadModel.Gain, Cdata, Scortex.Sc);
+    action                          = 'anat';
+    save_output_files(base_path, modality, subID, HeadModels, Cdata, Shead, Sout, Sinn, Scortex, AQCI, action);
+
     subjects                    = dir(eeglab_path);
     subjects(ismember({subjects.name},{'.','..'})) = [];
     for e=1:length(subjects)
-        subject                 = subjects(e);
+        subject                 = subjects(e);        
         subID                   = subject.name;
+        disp(strcat("-->> Saving subject: ",subID));
+        disp("--------------------------------------------------------------------------");
         EEG_path                = fullfile(eeglab_path,subID);
         HeadModels              = rawHeadModels;
         Cdata                   = rawCdata;
@@ -72,7 +97,7 @@
         participant                         = CiftiStorm.Template;
         participant.SubID                   = subID;
         participant.Status                  = "Completed";
-        participant.FileInfo                = strcat(subID,".mat");
+        participant.FileInfo                = strcat(subID,".json");
         participant.Process(end+1).Name     = "Integration";
         participant.Process(end).Status     = "Completed";
         participant.Process(end).Error      = [];