Updating visual components

README.md

@@ -18,7 +18,7 @@ A pipeline to integrate “legacy” datasets into a Human Connectome Project (H
     - name         --> Processing name
     - bst_config   --> Configuration structure for Brainstorm processing
         - protocol_name  --> Brainstorm protocol name
-        - protocol_reset --> Reset the protocol information if the protocol already exists in the Brainstorm database (true|false)
+        - reset_protocol --> Reset the protocol information if the protocol already exists in the Brainstorm database (true|false)
         - bst_path       --> Brainstorm Toolbox root directory
         - db_path        --> Path to create the Brainstorm database. (local) Will create it in the user's home directory. Define a real path in another case.
         - after_MaQC     --> Define as false to the first processing and true after channel correction to recompute the Headmodel and the Leadfield.
@@ -48,10 +48,8 @@ A pipeline to integrate “legacy” datasets into a Human Connectome Project (H
               - base_path           --> FSL Bet root directory
         - layer_desc         --> Layer descriptor structure
             - desc                --> Options <<white>> OR <<midthickness>> OR <<pial>> OR <<bigbrain>> multilayer like bigbrain OR <<fs_LR>> like HCP FSAve (three layers).
-        - surfaces_resolution --> Numbers of vertices for downsampling each surface
-            - nverthead     --> Scalp's number of vertices. Default: 8000
-            - nvertskull    --> Skull's number of vertices. Default: 8000
-            - nvertcortex   --> Cortex's number of vertices. Default: 8000        
+        - surfaces_resolution --> Numbers of vertices for downsampling the surface
+            - nvertices           --> Number of vertices. Default: 8000        
 
 ## Import channel process [[File]](https://github.com/CCC-members/CiftiStorm/blob/master/cfs_properties/process_import_channel.json)
     - channel_type    -->  Select the type of import channel process to be used. <<1>> Use raw data. <<2>> Use BST default template

bst_templates/bst_default_anatomy.json

@@ -1 +1 @@
-[    {        "name":"ICBM152",        "filePath":"D:/Tools/brainstorm3/defaults/anatomy/ICBM152"    },    {        "name":"BCI-DNI_BrainSuite_2016",        "filePath":"C:/Users/Ariosky/.brainstorm/defaults/anatomy/BCI-DNI_BrainSuite_2016.zip"    },    {        "name":"BCI-DNI_BrainSuite_2020",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=BCI-DNI_BrainSuite_2020"    },    {        "name":"Colin27_4NIRS",        "filePath":"C:/Users/Ariosky/.brainstorm/defaults/anatomy/Colin27_4NIRS.zip"    },    {        "name":"Colin27_2016",        "filePath":"C:/Users/Ariosky/.brainstorm/defaults/anatomy/Colin27_2016.zip"    },    {        "name":"Colin27_BrainSuite_2016",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_BrainSuite_2016"    },    {        "name":"FSAverage_2016",        "filePath":"C:/Users/Ariosky/.brainstorm/defaults/anatomy/FSAverage_2016.zip"    },    {        "name":"FsAverage_2020",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=FSAverage_2020"    },    {        "name":"ICBM152_2019",        "filePath":"C:/Users/Ariosky/.brainstorm/defaults/anatomy/ICBM152_2019.zip"    },    {        "name":"ICBM152_BrainSuite_2016",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_BrainSuite_2016"    },    {        "name":"Kabdebon_7w",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Kabdebon_7w"    },    {        "name":"Oreilly_0.5m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_0.5m"    },    {        "name":"Oreilly_1m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_1m"    },    {        "name":"Oreilly_2m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_2m"    },    {        "name":"Oreilly_3m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_3m"    },    {        "name":"Oreilly_4.5m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_4.5m"    },    {        "name":"Oreilly_6m",        "filePath":"C:/Users/Ariosky/.brainstorm/defaults/anatomy/Oreilly_6m.zip"    },    {        "name":"Oreilly_7.5m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_7.5m"    },    {        "name":"Oreilly_9m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_9m"    },    {        "name":"Oreilly_10.5m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_10.5m"    },    {        "name":"Oreilly_12m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_12m"    },    {        "name":"Oreilly_15m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_15m"    },    {        "name":"Oreilly_18m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_18m"    },    {        "name":"Oreilly_24m",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_24m"    },    {        "name":"USCBrain_BrainSuite_2020",        "filePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=USCBrain_BrainSuite_2020"    }]
+[    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2023b",        "Name":"ICBM152"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=BCI-DNI_BrainSuite_2020",        "Name":"BCI-DNI_BrainSuite_2020"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_2016",        "Name":"Colin27_2016"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_BrainSuite_2016",        "Name":"Colin27_BrainSuite_2016"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=FSAverage_2020",        "Name":"FsAverage_2020"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2019",        "Name":"ICBM152_2019"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2022",        "Name":"ICBM152_2022"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2023b",        "Name":"ICBM152_2023b"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_BrainSuite_2016",        "Name":"ICBM152_BrainSuite_2016"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Kabdebon_7w",        "Name":"Kabdebon_7w"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_0.5m_2021",        "Name":"Oreilly_0.5m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_1m_2021",        "Name":"Oreilly_1m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_2m_2021",        "Name":"Oreilly_2m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_3m_2021",        "Name":"Oreilly_3m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_4.5m_2021",        "Name":"Oreilly_4.5m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_6m_2021",        "Name":"Oreilly_6m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_7.5m_2021",        "Name":"Oreilly_7.5m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_9m_2021",        "Name":"Oreilly_9m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_10.5m_2021",        "Name":"Oreilly_10.5m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_12m_2021",        "Name":"Oreilly_12m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_15m_2021",        "Name":"Oreilly_15m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_18m_2021",        "Name":"Oreilly_18m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_24m_2021",        "Name":"Oreilly_24m_2021"    },    {        "FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=USCBrain_BrainSuite_2020",        "Name":"USCBrain_BrainSuite_2020"    }]

bst_templates/bst_default_mni_atlas.json

@@ -0,0 +1 @@
+[	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AAL2",	"Name":"AAL2",	"Info":"https://www.gin.cnrs.fr/en/tools/aal/"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AAL3",	"Name":"AAL3",	"Info":"https://www.gin.cnrs.fr/en/tools/aal/"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AICHA",	"Name":"AICHA",	"Info":"https://www.gin.cnrs.fr/en/tools/aicha"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brainnetome",	"Name":"Brainnetome",	"Info":"http://atlas.brainnetome.org/"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brainnetome_leaddbs",	"Name":"Brainnetome_leaddbs",	"Info":"http://atlas.brainnetome.org/"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brodmann",	"Name":"Brodmann",	"Info":"https://people.cas.sc.edu/rorden/mricro/lesion.html#brod"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Hammers",	"Name":"Hammers",	"Info":"http://brain-development.org/brain-atlases/adult-brain-atlases/"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Neuromorphometrics",	"Name":"Neuromorphometrics",	"Info":"https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Julich-Brain-v25",	"Name":"Julich-Brain-v25",	"Info":"https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6"},	{	"FilePath":"http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Schaefer2018",	"Name":"Schaefer2018",	"Info":"https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal"}]

cfs_properties/defaults/general_params.json

@@ -1,13 +1,18 @@
 {
     "description":"",
     "modality":"EEG",
-    "name":"HeadModel_CHBMP_NDC",
-    "description":"",
+    "dataset":{
+        "Name":"CHBM",
+        "Description":[
+            "CHBM Cl_eyes"
+        ]
+    },
     "colormap":"tools/Common/mycolormap.mat",
+
     "bst_config":{
         "description":"",
         "protocol_name":"HeadModel_CHBMP_NDC",
-        "protocol_reset":false,
+        "reset_protocol":false,
         "bst_path":"/mnt/Develop/Tools/brainstorm3",
         "db_path":"local",
         "after_MaQC":{

cfs_properties/defaults/process_import_anat.json

@@ -36,10 +36,8 @@
             "desc":"midthickness"
         },
         "surfaces_resolution":{
-            "description":"Numbers of vertices for downsample each surface: default <<8000>>",
-            "nverthead":8000,
-            "nvertskull":8000,
-            "nvertcortex":8000
+            "description":"Numbers of vertices for downsample the surfaces: default <<8000>>",
+            "nvertices":8000
         }
     }
 }

cfs_properties/defaults/process_import_channel.json

@@ -12,7 +12,6 @@
                 "base_path":"/mnt/Store/Data/Conectome/Sample/SubID",
                 "file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC",
                 "data_format":"4D",
-                "isfile":true,
                 "group_layout_name":"",
                 "channel_layout_name":""
             },

cfs_properties/functions/check_properties.m

@@ -310,27 +310,13 @@
     disp("--------------------------------------------------------------------------");
     disp('-->> Checking surface resolution');
     surf_resol = anat_params.common_params.surfaces_resolution;
-    if(isempty(surf_resol.nverthead) || surf_resol.nverthead < 2000 || surf_resol.nverthead > 15000)
-        fprintf(2,'The Head resolution have be between 2000 and 15000 vertices.\n');
-        disp('Please check the nverthead configuration in the process_import_anat.json file.');
+    if(isempty(surf_resol.nvertices) || surf_resol.nvertices > 15000)
+        fprintf(2,'The surfaces resolution have be between 2000 and 15000 vertices.\n');
+        disp('Please check the nvertices configuration in the process_import_anat.json file.');
         status = false;
         disp('-->> Process stopped!!!');
         return;
-    end
-    if(isempty(surf_resol.nvertskull) || surf_resol.nvertskull < 2000 || surf_resol.nvertskull > 15000)
-        fprintf(2,'The Skull resolution have be between 2000 and 15000 vertices.\n');
-        disp('Please check the nvertskull configuration in the process_import_anat.json file.');
-        status = false;
-        disp('-->> Process stopped!!!');
-        return;
-    end
-%     if(isempty(surf_resol.nvertcortex) || surf_resol.nvertcortex < 2000 || surf_resol.nvertcortex > 15000)
-%         fprintf(2,'The Cortex resolution have be between 2000 and 15000 vertices.\n');
-%         disp('Please check the nvertcortex configuration in the process_import_anat.json file.');
-%         status = false;
-%         disp('-->> Process stopped!!!');
-%         return;
-%     end
+    end   
 
     %%
     %% Checking import channel params

cfs_properties/general_params.json

@@ -1,13 +1,18 @@
 {
     "description":"",
     "modality":"EEG",
-    "name":"HeadModel_CHBMP_NDC",
-    "description":"",
+    "dataset":{
+        "Name":"CHBM",
+        "Description":[
+            "CHBM Dataset"
+        ]
+    },
     "colormap":"tools/Common/mycolormap.mat",
+
     "bst_config":{
         "description":"",
         "protocol_name":"HeadModel_CHBMP_NDC",
-        "protocol_reset":false,
+        "reset_protocol":false,
         "bst_path":"/mnt/Develop/Tools/brainstorm3",
         "db_path":"local",
         "after_MaQC":{

cfs_properties/process_import_anat.json

@@ -36,10 +36,8 @@
             "desc":"midthickness"
         },
         "surfaces_resolution":{
-            "description":"Numbers of vertices for downsample each surface: default <<8000>>",
-            "nverthead":8000,
-            "nvertskull":8000,
-            "nvertcortex":8000
+            "description":"Numbers of vertices for downsample the surfaces: default <<8000>>",
+            "nvertices":8000
         }
     }
 }

cfs_properties/process_import_channel.json

@@ -9,10 +9,9 @@
                 "name":"raw_data",
                 "description":"",
                 "subID_prefix":"",
-                "base_path":"/mnt/Store/Data/Conectome/Sample/SubID",
+                "base_path":"/mnt/Store/Data/Conectome/Sample",
                 "file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC",
                 "data_format":"4D",
-                "isfile":true,
                 "group_layout_name":"",
                 "channel_layout_name":""
             },

functions/processes/process_compute_surfaces.m

@@ -9,7 +9,7 @@
 anatomy_type    = properties.anatomy_params.anatomy_type.type_list{properties.anatomy_params.anatomy_type.type};
 layer_desc      = properties.anatomy_params.common_params.layer_desc.desc;
 mq_control      = properties.general_params.bst_config.after_MaQC.run;
-nVertCortex     = properties.anatomy_params.common_params.surfaces_resolution.nvertcortex;
+nvertices     = properties.anatomy_params.common_params.surfaces_resolution.nvertices;
 
 %%
 %% Getting report path
@@ -36,7 +36,7 @@
     CSurface = CSurfaces(i);
     if(~isempty(CSurface.name) && isequal(CSurface.type,'cortex'))
         comment                 = split(CSurface.comment,'_');
-        [NewFile,iSurface,I,J]  = tess_downsize(CSurface.filename, nVertCortex, 'reducepatch');
+        [NewFile,iSurface,I,J]  = tess_downsize(CSurface.filename, nvertices, 'reducepatch');
         CortexMat.Comment       = strcat('Cortex_',comment{2},'_low');
         if(isequal(layer_desc,lower('bigbrain')) || isequal(layer_desc,lower('fs_lr')))
             if(isequal(comment{2},'pial'))

functions/processes/process_create_subject.m

@@ -7,7 +7,7 @@
 %%
 %% Creating BST Protocol
 %%
-if(general_params.bst_config.protocol_reset)
+if(general_params.bst_config.reset_protocol)
     gui_brainstorm('DeleteProtocol',ProtocolName);
     bst_db_path = bst_get('BrainstormDbDir');
     if(isfolder(fullfile(bst_db_path,ProtocolName)))

functions/processes/utilities/apply_default_anat.m

@@ -3,9 +3,7 @@
 %%
 %% Surfaces resolution
 %%
-nVertHead       = properties.anatomy_params.common_params.surfaces_resolution.nverthead;
-nVertCortex     = properties.anatomy_params.common_params.surfaces_resolution.nvertcortex;
-nVertSkull      = properties.anatomy_params.common_params.surfaces_resolution.nvertskull;
+nvertices       = properties.anatomy_params.common_params.surfaces_resolution.nvertices;
 
 
 

functions/processes/utilities/import_HCP_surfaces.m

@@ -19,17 +19,16 @@
     midthickness_R      = surfaces{7};
     white_L             = surfaces{8};
     white_R             = surfaces{9};    
-    nVertHead           = surfaces_resolution.nverthead;
-    nVertSkull          = surfaces_resolution.nvertskull;
+    nvertices           = surfaces_resolution.nvertices;
 
     %% Importing non-brain surfacs
     bst_process('CallProcess', 'process_import_surfaces', [], [], ...
         'subjectname', subID, ...
         'headfile',    {head_file, 'MRI-MASK-MNI'}, ...
         'innerfile',   {innerskull_file, 'MRI-MASK-MNI'}, ...
         'outerfile',   {outerskull_file, 'MRI-MASK-MNI'}, ...
-        'nverthead',   nVertHead, ...
-        'nvertskull',  nVertSkull);
+        'nverthead',   nvertices, ...
+        'nvertskull',  nvertices);
 
     %% Importing Brain surfaces
     if(isequal(lower(layer_desc),'white') || isequal(lower(layer_desc),'midthickness') || isequal(lower(layer_desc),'pial'))