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cfs_properties/general_params.json

@@ -1 +1 @@
-{	"description":"",	"modality":"EEG",	"dataset":{	"Name":"CHBMP",	"Description":"HeadModel_Ariosdy"},	"bst_config":{	"description":"",	"protocol_name":"HeadModel_CHBMP",	"reset_protocol":false,	"bst_path":"/mnt/Develop/Tools/brainstorm3",	"db_path":"local",	"after_MaQC":{	"run":false}},	"output_path":"/mnt/Store/OneDrive/Ariosdy/Tesis/Application/Data",	"tmp_path":"local"}
+{    "description":"",    "modality":"EEG",    "dataset":{        "Name":"Barbados",        "Description":"Barbados dataset from Multinational Norms"    },    "bst_config":{        "description":"",        "protocol_name":"Barbados",        "reset_protocol":false,        "bst_path":"D:/Develop/Tools/brainstorm3",        "db_path":"local",        "after_MaQC":{            "run":false        }    },    "output_path":"E:/Data/MultinationalNorm/Barbados/derivatives",    "tmp_path":"local"}

cfs_properties/process_import_anat.json

@@ -1 +1 @@
-{    "description":"",    "anatomy_type":{        "description":"Select the type of anatomy to use. <<template>> Brainstorm default anatomy. <<individual>> HCP individual anatomy",        "type":"individual",        "type_list":[            {                "id":"default",                "name":"default_anatomy",                "description":"Select the Brainstorm anatomy template. See app/bst_default_anatomy.json file and select all params from there",                "template_name":"ICBM152_2023b",                "default_atlas":"Desikan-Killiany"            },{                "id":"individual",                "name":"hcp_anat_individual",                "description":"HCP individual anatomy",                "base_path":"/mnt/Store/OneDrive/Ariosdy/Tesis/Application/Data/ciftify",                "T1w_file_name":"T1w.nii.gz",                "Atlas_file_name":"aparc+aseg.nii.gz"            },{                "id":"template",                "name":"hcp_anat_template",                "description":"HCP anatomy to use as template for EEG dataset",                "base_path":"D:/Data/MIITRA/ciftify",                "template_name":"MIITRA",                "T1w_file_name":"T1w.nii.gz",                "Atlas_file_name":"aparc.a2009s+aseg.nii.gz"            }        ]    },    "common_params":{        "mri_transformation":{            "use_transformation":false,            "base_path":"/mnt/Store/Data/Conectome/Sample",            "file_name":"meg/SubID/MEG/anatomy/SubID_MEG_anatomy_transform.txt"        },        "non_brain_surfaces":{            "description":"FSL Bet command output",            "base_path":"/mnt/Store/OneDrive/Ariosdy/Tesis/Application/Data/fsl_bet"        },        "layer_desc":{            "description":"Layer descriptor. Options <<white>> OR <<midthickness>> OR <<pial>> OR <<bigbrain>> multilayer like bigbrain OR <<fs_LR>> like HCP FSAve (three layers).",            "desc":"Midthickness"        },        "surfaces_resolution":{            "description":"Numbers of vertices for downsample the surfaces: default <<8000>>",            "nvertices":8000        }    }}
+{    "description":"",    "anatomy_type":{        "description":"Select the type of anatomy to use. <<template>> Brainstorm default anatomy. <<individual>> HCP individual anatomy",        "type":"default",        "type_list":[            {                "id":"default",                "name":"default_anatomy",                "description":"Select the Brainstorm anatomy template. See app/bst_default_anatomy.json file and select all params from there",                "template_name":"ICBM152_2023b",                "default_atlas":"Desikan-Killiany"            },{                "id":"individual",                "name":"hcp_anat_individual",                "description":"HCP individual anatomy",                "base_path":"/mnt/Store/OneDrive/Ariosdy/Tesis/Application/Data/ciftify",                "T1w_file_name":"T1w.nii.gz",                "Atlas_file_name":"aparc+aseg.nii.gz"            },{                "id":"template",                "name":"hcp_anat_template",                "description":"HCP anatomy to use as template for EEG dataset",                "base_path":"D:/Data/MIITRA/ciftify",                "template_name":"MIITRA",                "T1w_file_name":"T1w.nii.gz",                "Atlas_file_name":"aparc.a2009s+aseg.nii.gz"            }        ]    },    "common_params":{        "mri_transformation":{            "use_transformation":false,            "base_path":"/mnt/Store/Data/Conectome/Sample",            "file_name":"meg/SubID/MEG/anatomy/SubID_MEG_anatomy_transform.txt"        },        "non_brain_surfaces":{            "description":"FSL Bet command output",            "base_path":"/mnt/Store/OneDrive/Ariosdy/Tesis/Application/Data/fsl_bet"        },        "layer_desc":{            "description":"Layer descriptor. Options <<white>> OR <<midthickness>> OR <<pial>> OR <<bigbrain>> multilayer like bigbrain OR <<fs_LR>> like HCP FSAve (three layers).",            "desc":"Midthickness"        },        "surfaces_resolution":{            "description":"Numbers of vertices for downsample the surfaces: default <<8000>>",            "nvertices":8000        }    }}

cfs_properties/process_integration.json

@@ -1 +1 @@
-{    "description":"Integration process for Structural and Functional Data",    "preproc_data":{        "description":"Select the base path for the  preprocessed EEG or MEG",        "base_path":"/mnt/Store/OneDrive/Ariosdy/Tesis/Application/Data/eeglab",        "event_file":"All",        "format":"set"    }}
+{    "description":"Integration process for Structural and Functional Data",    "preproc_data":{        "description":"Select the base path for the  preprocessed EEG or MEG",        "base_path":"E:/Data/MultinationalNorm/Barbados/derivatives/eeglab",        "event_file":"All",        "segment":"",        "format":"set"    }}

functions/cfs_process_interface.m

@@ -48,7 +48,7 @@
             if(isempty(sTemplate))
                 fprintf(2,strcat('\nBC-V-->> Error: The selected template name in process_import_anat.json is wrong \n'));
                 disp(strcat("Name: ",subjects.name));
                 disp(strcat("Please check the aviable anatomy templates in bst_template/bst_default_anatomy.json file"));
                 disp('-->> Process stopped!!!');
                 return;
             end 
@@ -165,6 +165,18 @@
     disp(strcat('CFS -->> Subject:' , subID, '. Processing finished.'));
     disp('==========================================================================');    
 end
+%%
+%% Getting participants metadata
+%%
+eeglab_path             = fullfile(properties.integration_params.preproc_data.base_path);
+participants_file = fullfile(eeglab_path,'Participants.json');
+if(isfile(participants_file))
+    copyfile(participants_file,fullfile(CiftiStorm.Location,'Participants.json'))
+end
+
+%%
+%% Saving dataset information
+%%
 disp(strcat('CFS -->> Saving Dataset.'));
 disp('==============================================================================');
 datasetFile = fullfile(CiftiStorm.Location,'CiftiStorm.json');

functions/export/StructFunct_integration.m

@@ -1,25 +1,25 @@
 function [MEEGs, HeadModels, Cdata] = StructFunct_integration(EEG_path, modality, HeadModels, Cdata)
 
-MEEGs = struct;
+
 EEG_file                = dir(EEG_path);
 EEG_file([EEG_file.isdir]==1) = [];
 if(~isempty(EEG_file))
     count = 1;
     for i=1:length(EEG_file)
         [~,filename,ext]      = fileparts(EEG_file(i).name);
         if(isequal(ext,'.set'))
-            MEEGs(count).EEG        = load(fullfile(EEG_file(i).folder,EEG_file(i).name),'-mat');
-            while(isfield( MEEGs(count).EEG,'EEG'))
-                 MEEGs(count).EEG = MEEGs(count).EEG.EEG;
+            MEEGs(count)      = load(fullfile(EEG_file(i).folder,EEG_file(i).name),'-mat');
+            while(isfield( MEEGs(count),'EEG'))
+                 MEEGs(count) = MEEGs(count).EEG;
             end
-            if(ischar(MEEGs(count).EEG.data))
+            if(ischar(MEEGs(count).data))
                 fid = fopen(fullfile(EEG_file(i).folder,strrep(EEG_file(i).name,'set','fdt')), 'r', 'ieee-le');
-                for trialIdx = 1:MEEGs(count).EEG.trials % In case the saved data are epoched, loop the process for each epoch. Thanks Ramesh Srinivasan!
-                    currentTrialData = fread(fid, [MEEGs(count).EEG.nbchan MEEGs(count).EEG.pnts], 'float32');
+                for trialIdx = 1:MEEGs(count).trials % In case the saved data are epoched, loop the process for each epoch. Thanks Ramesh Srinivasan!
+                    currentTrialData = fread(fid, [MEEGs(count).nbchan MEEGs(count).pnts], 'float32');
                     data{trialIdx} = currentTrialData; % Data dimentions are: electrodes, time points, and trials (the last one is for epoched data)
                 end
                 fclose(fid);
-                MEEGs(count).EEG.data = data;
+                MEEGs(count).data = data;
             end
             if(~contains(filename,'task'))
                 filename_parts = split(filename,'_');
@@ -32,13 +32,13 @@
             count = count + 1;
         end
     end
-    MEEG                    = MEEGs(1).EEG;
+    MEEG                    = MEEGs(1);
 
     %%
     %% Filter Channels and LeadField by Preprocessed MEEG
     %%
     if(isequal(modality,'EEG'))
-        labels              = {MEEGs(1).EEG.chanlocs(:).labels};
+        labels              = {MEEGs(1).chanlocs(:).labels};
     elseif(isequal(modality,'MEG'))
         labels              = MEEG.labels;
     else

functions/export/save_output_files.m

@@ -36,16 +36,18 @@
 if(isequal(action,'all'))
     disp ("-->> Saving MEEG file");
     for i=1:length(MEEGs)
-        EEG = MEEGs(i).EEG;
+        EEG = MEEGs(i);
         save(fullfile(output_subject_dir,subject_info.meeg_dir{i}),'-struct','EEG');
     end
 end
 
 %%
 %% Export subject from protocol
 %%
-disp ("-->> Saving Brainstorm subject file");
-process_export_subject(output_subject_dir, subID, MEEGs(1));
+if(isequal(action,'all'))
+    disp ("-->> Saving Brainstorm subject file");
+    process_export_subject(output_subject_dir, subID, MEEGs(1));
+end
 disp ("-->> Saving channel file");
 save(fullfile(output_subject_dir,subject_info.channel_dir),'-struct','Cdata');
 disp ("-->> Saving leadfield file");

functions/processes/process_export_subject.m

@@ -1,5 +1,8 @@
-function process_export_subject(output_subject_dir, subID, EEG)
+function process_export_subject(output_subject_dir, subID, EEG, varargin)
 
+for i=1:length(varargin)
+    eval([inputname(i+4) '= varargin{i};']);
+end
 
 %%
 %% Update subject protocol with preprocessed data
@@ -20,7 +23,7 @@ function process_export_subject(output_subject_dir, subID, EEG)
 end
 HeadModel = load(fullfile(ProtocolInfo.STUDIES, sStudies.HeadModel.FileName));
 Cdata     = load(fullfile(ProtocolInfo.STUDIES, sStudies.Channel.FileName));
-[Cdata_r, Gain] = remove_channels_by_preproc_data({EEG.EEG.chanlocs.labels}, Cdata, HeadModel.Gain);
+[Cdata_r, Gain] = remove_channels_by_preproc_data({EEG.chanlocs.labels}, Cdata, HeadModel.Gain);
 
 HeadModel.Gain = Gain;
 save(fullfile(ProtocolInfo.STUDIES, sStudies.HeadModel.FileName),'-struct','HeadModel');
@@ -40,6 +43,8 @@ function process_export_subject(output_subject_dir, subID, EEG)
 subject_file    = fullfile(output_subject_dir,'brainstorm',strcat(subID,'.zip'));
 export_protocol(iProtocol, iSubject, subject_file);
 
+
+
 %%
 %% Save and display report
 %%

functions/processes/process_integration.m

@@ -78,19 +78,27 @@
     action                          = 'anat';
     save_output_files(base_path, modality, subID, HeadModels, Cdata, Shead, Sout, Sinn, Scortex, AQCI, action);
 
-    subjects                    = dir(eeglab_path);
+    subjects                        = dir(eeglab_path);
     subjects(ismember({subjects.name},{'.','..'})) = [];
     for e=1:length(subjects)
-        subject                 = subjects(e);        
-        subID                   = subject.name;
+        subject                     = subjects(e);        
+        subID                       = subject.name;
         disp(strcat("-->> Saving subject: ",subID));
         disp("--------------------------------------------------------------------------");
-        EEG_path                = fullfile(eeglab_path,subID);
-        HeadModels              = rawHeadModels;
-        Cdata                   = rawCdata;
-        [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);
+        EEG_path                    = fullfile(eeglab_path,subID);
+        HeadModels                  = rawHeadModels;
+        Cdata                       = rawCdata;
+        [MEEGs,HeadModels,Cdata]    = StructFunct_integration(EEG_path, modality, HeadModels, Cdata);
+        AQCI                        = AutomaticQCI(HeadModels.HeadModel.Gain, Cdata, Scortex.Sc);
+        templateName                = CiftiStorm.Template.SubID;
+
+        %%
+        %% Dupicate subject if template or default
+        %%
+        [newTemplateName, Messages]        = process_duplicate('DuplicateSubject', templateName, '_copy');
+        db_rename_subject(newTemplateName, subID, 0);
+        action = 'all';
+        save_output_files(base_path, modality, subID, MEEGs, HeadModels, Cdata, Shead, Sout, Sinn, Scortex, AQCI, action);    
 
         participant                         = CiftiStorm.Template;
         participant.SubID                   = subID;