CCC-members · arioskyag · May 23, 2024 · May 23, 2024
diff --git a/cfs_properties/process_import_channel.json b/cfs_properties/process_import_channel.json
@@ -1 +1 @@
-{	"description":"",	"channel_type":{	"description":"Select the type of import channel process to be used. <<raw>> Use raw data. <<default>> Use BST default template ",	"type":"default",	"type_list":[	{	"id":"raw",	"name":"raw_data",	"description":"",	"subID_prefix":"",	"base_path":"/mnt/Store/Data/Conectome/Sample",	"file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC",	"data_format":"4D",	"group_layout_name":"",	"channel_layout_name":""},{	"id":"default",	"name":"import_channel",	"description":"Select the group and name of the sensor layout. See bst_defaults/bst_eeg_layouts.json file and select all params from there",	"group_layout_name":"ICBM152",	"channel_layout_name":"ASA 10-05 343"}]},	"channel_label_file":""}
+{    "description":"",    "channel_type":{        "description":"Select the type of import channel process to be used. <<raw>> Use raw data. <<default>> Use BST default template ",        "type":"default",        "type_list":[            {                "id":"raw",                "name":"raw_data",                "description":"",                "subID_prefix":"",                "base_path":"/mnt/Store/Data/Conectome/Sample",                "file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC",                "data_format":"4D",                "group_layout_name":"",                "channel_layout_name":""            },{                "id":"default",                "name":"import_channel",                "description":"Select the group and name of the sensor layout. See bst_defaults/bst_eeg_layouts.json file and select all params from there",                "group_layout_name":"ICBM152",                "channel_layout_name":"10-20 19"            }        ]    },    "channel_label_file":""}

diff --git a/external/script_tess_force_envelope.m b/external/script_tess_force_envelope.m
@@ -1,4 +1,4 @@
-function [NewTessFile, iSurface] = script_tess_force_envelope(TessFile, EnvFile, subject_report_path)
+function [NewTessFile, iSurface] = script_tess_force_envelope(TessFile, EnvFile)
 % TESS_FORCE_ENVELOPE: Forces the vertices of a surface to fit entirely in an envelope.
 %
 % USAGE:  [NewTessFile, iSurface] = tess_force_envelope(TessFile, EnvFile)
@@ -160,6 +160,7 @@
 
     % Display modified surface
     if(getGlobalVerbose())
+        report_path = get_report_path(CiftiStorm, subID);
         hFig_after = view_surface(NewTessFile, [], [], 'NewFigure');
         panel_surface('SetSurfaceEdges', hFig_after, 1, 1);
         view_surface(EnvFile, [], [], hFig_after);
@@ -174,7 +175,7 @@
                 'colorbars',{'off','off','off','off'},...
                 'view_orient',{[0,90],[1,270],[1,180],[0,360]});
             bst_report('Snapshot',fig_out,[],'Cortex view before force the vertices inside of InnerSkull.', [200,200,900,700]);
-            savefig( hFig_before,fullfile(subject_report_path,fig_text));
+            savefig( hFig_before,fullfile(report_path,fig_text));
             close(fig_out);
             fig_text    =  strcat("Distance corrected - ",desc{2});
             figures     = {hFig_after, hFig_after, hFig_after, hFig_after};
@@ -183,7 +184,7 @@
                 'colorbars',{'off','off','off','off'},...
                 'view_orient',{[0,90],[1,270],[1,180],[0,360]});
             bst_report('Snapshot',fig_out,[],'Cortex view. All cortex vertices are already inside the inner skull.', [200,200,900,700]);
-            savefig( hFig_after,fullfile(subject_report_path,fig_text));
+            savefig( hFig_after,fullfile(report_path,fig_text));
             close(fig_out);
         end
         close([hFig_before,hFig_after]);

diff --git a/functions/cfs_process_interface.m b/functions/cfs_process_interface.m
@@ -41,6 +41,7 @@
         subjects                = subjects.Subject;
     case false
         if(isequal(lower(anatomy_type.id),'default'))
+            CiftiStorm.Location = fullfile(general_params.output_path,strcat('ciftistorm-',anatomy_type.template_name));
             subjects.name       = anatomy_type.template_name;
             sTemplates          = bst_get('AnatomyDefaults');
             sTemplate           = sTemplates(find(strcmpi(subjects.name, {sTemplates.Name}),1));

diff --git a/functions/export/create_report_path.m b/functions/export/create_report_path.m
@@ -1,27 +1,20 @@
-function create_report_path(properties, subID)
+function create_report_path(CiftiStorm, subID)
 
 %%
 %% Checking the report output structure
 %%
-ProtocolName        = properties.general_params.bst_config.protocol_name;
-output_path         = properties.general_params.output_path;
+output_path         = CiftiStorm.Location;
 if(output_path == "local")
     output_path     = pwd;
 end
 if(~isfolder(output_path))
     mkdir(output_path);
 end
-if(~isfolder(fullfile(output_path,'ciftistorm')))
-    mkdir(fullfile(output_path,'ciftistorm'));
+if(~isfolder(fullfile(output_path,'Reports')))
+    mkdir(fullfile(output_path,'Reports'));
 end
-if(~isfolder(fullfile(output_path,'ciftistorm',subID)))
-    mkdir(fullfile(output_path,'ciftistorm',subID));
-end
-if(~isfolder(fullfile(output_path,'brainstorm')))
-    mkdir(fullfile(output_path,'brainstorm'));
-end
-if(~isfolder(fullfile(output_path,'brainstorm','Reports')))
-    mkdir(fullfile(output_path,'brainstorm','Reports'));
+if(~isfolder(fullfile(output_path,'Reports',subID)))
+    mkdir(fullfile(output_path,'Reports',subID));
 end
 end
 
diff --git a/functions/export/export_subject_structure.m b/functions/export/export_subject_structure.m
@@ -1,4 +1,4 @@
-function export_error = export_subject_structure(properties,subID,CSurfaces,sub_to_FSAve, AQCI)
+function export_error = export_subject_structure(CiftiStorm,subID,CSurfaces,sub_to_FSAve, AQCI)
 
 %%
 %% Get Protocol information
@@ -8,7 +8,7 @@
 % Get subject directory
 ProtocolInfo    = bst_get('ProtocolInfo');
 sSubject        = bst_get('Subject', subID);
-output_path     = properties.general_params.output_path;
+base_path       = CiftiStorm.Location;
 
 
 % Get the current Study
@@ -46,7 +46,6 @@
 %%
 %% Saving files in BC-VARETA Structure
 %%
-base_path = fullfile(output_path,'ciftistorm');
 save_output_files(base_path, modality, subID, HeadModels, Cdata, Shead, Sout, Sinn, Scortex, AQCI);
 
 end

diff --git a/functions/export/get_report_path.m b/functions/export/get_report_path.m
@@ -1,14 +1,13 @@
-function report_path = get_report_path(properties, subID)
+function report_path = get_report_path(CiftiStorm, subID)
 
 %%
 %% Checking the report output structure
 %%
-ProtocolName        = properties.general_params.bst_config.protocol_name;
-output_path         = properties.general_params.output_path;
+output_path         = CiftiStorm.Location;
 if(output_path == "local")
     output_path     = pwd;
 end
-report_path = fullfile(output_path,'brainstorm','Reports',subID);
+report_path = fullfile(output_path,'Reports',subID);
 if(~isfolder(report_path))
     mkdir(report_path);
 end

diff --git a/functions/processes/process_canonical_surfaces.m b/functions/processes/process_canonical_surfaces.m
@@ -2,11 +2,6 @@
 
 errMessage  = [];
 mq_control  = properties.general_params.bst_config.after_MaQC.run;
-%%
-%% Getting report path
-%%
-report_path = get_report_path(properties, subID);
-
 %%
 %% Compute SPM canonical surfaces
 %%
@@ -21,6 +16,7 @@
 %%
 % Get subject definition and subject files
 if(getGlobalVerbose())
+    report_path = get_report_path(CiftiStorm, subID);
     sSubject    = bst_get('Subject', subID);
     MriFile     = sSubject.Anatomy(sSubject.iAnatomy).FileName;
     ScalpFile   = sSubject.Surface(sSubject.iScalp).FileName;

diff --git a/functions/processes/process_compute_surfaces.m b/functions/processes/process_compute_surfaces.m
@@ -11,11 +11,6 @@
 mq_control      = properties.general_params.bst_config.after_MaQC.run;
 nvertices     = properties.anatomy_params.common_params.surfaces_resolution.nvertices;
 
-%%
-%% Getting report path
-%%
-report_path = get_report_path(properties, subID);
-
 %%
 %% Compute surfaces like BigBrain
 %%
@@ -92,7 +87,7 @@
         if(~isempty(CSurface.name)  && isequal(CSurface.type,'cortex'))
             CortexFile                  = Surfaces(CSurface.iSurface).FileName;
             % [NewTessFile, iSurface]     = tess_force_envelope(CortexFile, InnerSkullFile);
-            [NewTessFile, iSurface]     = script_tess_force_envelope(CortexFile, InnerSkullFile, report_path);
+            [NewTessFile, iSurface]     = script_tess_force_envelope(CortexFile, InnerSkullFile);
             if(~isempty(iSurface))
                 CSurfaces(i).comment    = strcat(CSurface.comment,'_fix');
                 CSurfaces(i).iSurface   = iSurface;
@@ -163,6 +158,7 @@
 %% Quality control
 %%
 if(getGlobalVerbose())
+    report_path = get_report_path(CiftiStorm, subID);
     [sSubject, ~]       = bst_get('Subject', subID);
     Surfaces            = sSubject.Surface;
     for i=1:length(CSurfaces)

diff --git a/functions/processes/process_create_subject.m b/functions/processes/process_create_subject.m
@@ -31,7 +31,9 @@
     end
     db_reload_database('current');
     db_add_subject(subID);
-    create_report_path(properties, subID);
+    if(getGlobalVerbose())
+        create_report_path(CiftiStorm, subID);
+    end
 else
     gui_brainstorm('UpdateProtocolsList');
     iProtocol = bst_get('Protocol', ProtocolName);

diff --git a/functions/processes/process_export_subject.m b/functions/processes/process_export_subject.m
@@ -2,7 +2,7 @@
 
 errMessage      = [];
 if(isequal(properties.anatomy_params.anatomy_type.id,'individual'))
-    output_path     = fullfile(properties.general_params.output_path,'brainstorm');
+    output_path     = CiftiStorm.Location;
 else
     template_name = properties.anatomy_params.anatomy_type.template_name;
     output_path = fullfile(properties.general_params.output_path,strcat('brainstorm-',template_name));
@@ -26,7 +26,7 @@
 %%
 if(getGlobalVerbose())
     disp("-->> Export BST Report");
-    report_path     = get_report_path(properties, subID);
+    report_path     = get_report_path(CiftiStorm, subID);
     ReportFile      = bst_report('Save', []);
     bst_report('Export',  ReportFile, fullfile(report_path,[subID,'.html'])); 
 end

diff --git a/functions/processes/process_gen_bem_surfaces.m b/functions/processes/process_gen_bem_surfaces.m
@@ -2,10 +2,6 @@
 
 errMessage  = [];
 mq_control  = properties.general_params.bst_config.after_MaQC.run;
-%%
-%% Getting report path
-%%
-report_path = get_report_path(properties, subID);
 
 %%
 %% Compute BEM Surfaces
@@ -48,6 +44,7 @@
 %% Quality control
 %%
 if(getGlobalVerbose())
+    report_path = get_report_path(CiftiStorm, subID);
     sSubject    = bst_get('Subject', subID);
     Surfaces    = sSubject.Surface;
     CortexFile  = Surfaces(sSubject.iCortex).FileName;

diff --git a/functions/processes/process_import_anat.m b/functions/processes/process_import_anat.m
@@ -85,14 +85,12 @@
     end   
 end
 
-%%
-%% Getting report path
-%%
-report_path = get_report_path(properties, subID);
+
 %%
 %% Quality control
 %%
 % Get MRI file and surface files
+report_path = get_report_path(CiftiStorm, subID);
 if(getGlobalVerbose())
     [sSubject,~]    = bst_get('Subject', subID);
     MriFile         = sSubject.Anatomy(sSubject.iAnatomy).FileName;

diff --git a/functions/processes/process_import_atlas.m b/functions/processes/process_import_atlas.m
@@ -3,7 +3,6 @@
 %%
 %% Getting report path and params
 %%
-report_path     = get_report_path(properties, subID);
 errMessage      = [];
 anatomy_type    = properties.anatomy_params.anatomy_type;
 type            = anatomy_type.id;
@@ -54,6 +53,7 @@
         %% Quality control
         %%
         if(getGlobalVerbose())
+            report_path     = get_report_path(CiftiStorm, subID);
             panel_scout('SetScoutsOptions', 0, 0, 1, 'all', 1, 0, 0, 0);
             panel_scout('UpdateScoutsDisplay', 'all');
             panel_scout('SetScoutContourVisible', 0, 0);

diff --git a/functions/processes/process_import_chann.m b/functions/processes/process_import_chann.m
@@ -9,12 +9,6 @@
 sSubject        = bst_get('Subject', subID);
 type            = properties.channel_params.channel_type.id;
 
-
-%%
-%% Getting report path
-%%
-report_path     = get_report_path(properties, subID);
-
 if(~mq_control)    
     %%
     %% ===== IMPORT CHANNEL =====
@@ -151,6 +145,7 @@
 %% 
 %%
 if(getGlobalVerbose())
+    report_path     = get_report_path(CiftiStorm, subID);
     if(isequal(properties.general_params.modality,'EEG'))
         hFigMri16   = script_view_mri_3d(MriFile, [], [], [], 'front');
         hFigMri16   = view_channels(ChannelFile, 'EEG', 1, 0, hFigMri16, 1);

diff --git a/functions/processes/process_integration.m b/functions/processes/process_integration.m
@@ -3,14 +3,8 @@
 % Get subject directory
 ProtocolInfo    = bst_get('ProtocolInfo');
 sSubject        = bst_get('Subject', subID);
-general_params  = properties.general_params;
+base_path       = CiftiStorm.Location;
 
-if(isequal(properties.anatomy_params.anatomy_type.id,'individual'))
-    base_path     = fullfile(general_params.output_path,'ciftistorm');
-else
-    template_name = properties.anatomy_params.anatomy_type.template_name;
-    base_path = fullfile(general_params.output_path,strcat('ciftistorm-',template_name));
-end
 
 % Get the current Study
 [sStudies, ~]   = bst_get('StudyWithSubject', sSubject.FileName, 'intra_subject');
@@ -68,12 +62,11 @@
     CiftiStorm.Participants(end).Process(end).Error     = [];
 else
     CiftiStorm.Template = CiftiStorm.Participants;
-    disp(strcat("-->> Saving anatomy template: ",template_name));
+    disp(strcat("-->> Saving anatomy template: ",subID));
     disp("--------------------------------------------------------------------------");
-    CiftiStorm.Template.SubID       = template_name;
+    CiftiStorm.Template.SubID       = subID;
     CiftiStorm.Template.Status      = "Anatomy";
-    CiftiStorm.Template.FileInfo    = strcat(template_name,'.json');
-    subID                           = template_name;
+    CiftiStorm.Template.FileInfo    = strcat(subID,'.json');
     HeadModels                      = rawHeadModels;
     Cdata                           = rawCdata;
     AQCI                            = AutomaticQCI(HeadModels.HeadModel.Gain, Cdata, Scortex.Sc);
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{ "description":"", "channel_type":{ "description":"Select the type of import channel process to be used. <<raw>> Use raw data. <<default>> Use BST default template ", "type":"default", "type_list":[ { "id":"raw", "name":"raw_data", "description":"", "subID_prefix":"", "base_path":"/mnt/Store/Data/Conectome/Sample", "file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC", "data_format":"4D", "group_layout_name":"", "channel_layout_name":""},{ "id":"default", "name":"import_channel", "description":"Select the group and name of the sensor layout. See bst_defaults/bst_eeg_layouts.json file and select all params from there", "group_layout_name":"ICBM152", "channel_layout_name":"ASA 10-05 343"}]}, "channel_label_file":""}
		{ "description":"", "channel_type":{ "description":"Select the type of import channel process to be used. <<raw>> Use raw data. <<default>> Use BST default template ", "type":"default", "type_list":[ { "id":"raw", "name":"raw_data", "description":"", "subID_prefix":"", "base_path":"/mnt/Store/Data/Conectome/Sample", "file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC", "data_format":"4D", "group_layout_name":"", "channel_layout_name":"" },{ "id":"default", "name":"import_channel", "description":"Select the group and name of the sensor layout. See bst_defaults/bst_eeg_layouts.json file and select all params from there", "group_layout_name":"ICBM152", "channel_layout_name":"10-20 19" } ] }, "channel_label_file":""}
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