From 23c9135d257e7e47eec5a29bfc8002b9bacc4749 Mon Sep 17 00:00:00 2001
From: Ariosky Areces Gonzalez <48639831+arioskyag@users.noreply.github.com>
Date: Mon, 18 Nov 2024 18:11:36 +0800
Subject: [PATCH 1/2] Updating

---
 cfs_properties/general_params.json           |  2 +-
 cfs_properties/process_import_anat.json      |  2 +-
 cfs_properties/process_integration.json      |  2 +-
 functions/export/StructFunct_integration.m   | 20 +++++++--------
 functions/export/save_output_files.m         |  8 +++---
 functions/processes/process_export_subject.m |  9 +++++--
 functions/processes/process_integration.m    | 26 +++++++++++++-------
 7 files changed, 42 insertions(+), 27 deletions(-)

diff --git a/cfs_properties/general_params.json b/cfs_properties/general_params.json
index d424a32..5565ff5 100644
--- a/cfs_properties/general_params.json
+++ b/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"
}
\ No newline at end of file
+{
    "description":"",
    "modality":"EEG",
    "dataset":{
        "Name":"Neuroimmunology",
        "Description":"Neuroimmunology dataset. Exploratory analysis"
    },
    "bst_config":{
        "description":"",
        "protocol_name":"HeadModel_NI",
        "reset_protocol":false,
        "bst_path":"/mnt/Develop/Tools/brainstorm3",
        "db_path":"local",
        "after_MaQC":{
            "run":false
        }
    },
    "output_path":"/mnt/Store/SharePoint/CCC-Internal Project - Neuroimmunology - 文档/Neuroimmunology/Data/Exploratory_analysis",
    "tmp_path":"local"
}
\ No newline at end of file
diff --git a/cfs_properties/process_import_anat.json b/cfs_properties/process_import_anat.json
index 70ec663..deade9c 100644
--- a/cfs_properties/process_import_anat.json
+++ b/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
        }
    }
}
\ No newline at end of file
+{
    "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
        }
    }
}
\ No newline at end of file
diff --git a/cfs_properties/process_integration.json b/cfs_properties/process_integration.json
index d07c9c0..2fe33d0 100644
--- a/cfs_properties/process_integration.json
+++ b/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"
    }
}
\ No newline at end of file
+{
    "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/SharePoint/CCC-Internal Project - Neuroimmunology - 文档/Neuroimmunology/Data/Exploratory_analysis/eeglab",
        "event_file":"All",
        "segment":"All",
        "format":"set"
    }
}
\ No newline at end of file
diff --git a/functions/export/StructFunct_integration.m b/functions/export/StructFunct_integration.m
index 694d171..dff0b56 100644
--- a/functions/export/StructFunct_integration.m
+++ b/functions/export/StructFunct_integration.m
@@ -1,6 +1,6 @@
 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))
@@ -8,18 +8,18 @@
     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
diff --git a/functions/export/save_output_files.m b/functions/export/save_output_files.m
index 819e197..505179e 100644
--- a/functions/export/save_output_files.m
+++ b/functions/export/save_output_files.m
@@ -36,7 +36,7 @@
 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
@@ -44,8 +44,10 @@
 %%
 %% 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");
diff --git a/functions/processes/process_export_subject.m b/functions/processes/process_export_subject.m
index e2b14c3..962ac91 100644
--- a/functions/processes/process_export_subject.m
+++ b/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
 %%
diff --git a/functions/processes/process_integration.m b/functions/processes/process_integration.m
index 0ab258d..689b64b 100644
--- a/functions/processes/process_integration.m
+++ b/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;

From 6a115b0f7e67958dcc1c9755e4380d55496bf531 Mon Sep 17 00:00:00 2001
From: Ariosky Areces Gonzalez <48639831+arioskyag@users.noreply.github.com>
Date: Wed, 18 Dec 2024 15:41:23 +0700
Subject: [PATCH 2/2] update

---
 cfs_properties/general_params.json      |  2 +-
 cfs_properties/process_integration.json |  2 +-
 functions/cfs_process_interface.m       | 12 ++++++++++++
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/cfs_properties/general_params.json b/cfs_properties/general_params.json
index 5565ff5..dade6ba 100644
--- a/cfs_properties/general_params.json
+++ b/cfs_properties/general_params.json
@@ -1 +1 @@
-{
    "description":"",
    "modality":"EEG",
    "dataset":{
        "Name":"Neuroimmunology",
        "Description":"Neuroimmunology dataset. Exploratory analysis"
    },
    "bst_config":{
        "description":"",
        "protocol_name":"HeadModel_NI",
        "reset_protocol":false,
        "bst_path":"/mnt/Develop/Tools/brainstorm3",
        "db_path":"local",
        "after_MaQC":{
            "run":false
        }
    },
    "output_path":"/mnt/Store/SharePoint/CCC-Internal Project - Neuroimmunology - 文档/Neuroimmunology/Data/Exploratory_analysis",
    "tmp_path":"local"
}
\ No newline at end of file
+{
    "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"
}
\ No newline at end of file
diff --git a/cfs_properties/process_integration.json b/cfs_properties/process_integration.json
index 2fe33d0..521c9e2 100644
--- a/cfs_properties/process_integration.json
+++ b/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/SharePoint/CCC-Internal Project - Neuroimmunology - 文档/Neuroimmunology/Data/Exploratory_analysis/eeglab",
        "event_file":"All",
        "segment":"All",
        "format":"set"
    }
}
\ No newline at end of file
+{
    "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"
    }
}
\ No newline at end of file
diff --git a/functions/cfs_process_interface.m b/functions/cfs_process_interface.m
index 3b679dc..1798358 100644
--- a/functions/cfs_process_interface.m
+++ b/functions/cfs_process_interface.m
@@ -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');