Merge pull request #148 from CCC-members/develop

Updating template
CCC-members · Jun 14, 2024 · dc1984f · dc1984f
2 parents 0e415df + 52740bf
commit dc1984f
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Showing 3 changed files with 21 additions and 4 deletions.
diff --git a/cfs_properties/functions/check_properties.m b/cfs_properties/functions/check_properties.m
@@ -83,9 +83,9 @@
     anat_params = properties.anatomy_params;
 
     % Check default template configuration
-    if(isequal(lower(anat_params.anatomy_type.id),'template'))
+    if(isequal(lower(anat_params.anatomy_type.id),'default'))
         disp("--------------------------------------------------------------------------");
-        disp('-->> Checking template configuration');
+        disp('-->> Checking default configuration');
         selected_anatomy = anat_params.anatomy_type;
         template_name = selected_anatomy.template_name;
         defaults = jsondecode(fileread(fullfile('bst_defaults','bst_default_anatomy.json')));
@@ -175,6 +175,23 @@
             end
         end
     end
+
+    if(isequal(lower(anat_params.anatomy_type.id),'template'))
+        disp("--------------------------------------------------------------------------");
+        disp('-->> Checking template configuration');
+        selected_anatomy = anat_params.anatomy_type;
+        template_name = selected_anatomy.template_name;
+        subjects = dir(selected_anatomy.base_path);
+        if(~contains(template_name, {subjects.name}))
+            fprintf(2,strcat('\nBC-V-->> Error: The selected template name in process_import_anat.json is wrong \n'));
+            disp(strcat("Name: ",template_name));
+            disp(strcat("Please check the available anatomy templates in bst_template/bst_default_anatomy.json file"));
+            status = false;
+            disp('-->> Process stopped!!!');
+            return;
+        end
+    end
+
     % Check MRI transform configuration
     mri_transform = anat_params.common_params.mri_transformation;
     if(mri_transform.use_transformation)

diff --git a/cfs_properties/general_params.json b/cfs_properties/general_params.json
@@ -1 +1 @@
-{    "description":"",    "modality":"EEG",    "dataset":{        "Name":"CHBMP",        "Description":"ICBM152"    },    "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/Data/Data_report/Test",    "tmp_path":"local"}
+{    "description":"",    "modality":"EEG",    "dataset":{        "Name":"CHBMP",        "Description":"ICBM152"    },    "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/Data/Talia/MIITRA",    "tmp_path":"local"}

diff --git 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":"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/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/ciftify",                "T1w_file_name":"T1w.nii.gz",                "Atlas_file_name":"aparc.a2009s+aseg.nii.gz"            },{                "id":"template",                "name":"hcp_anat_template",                "description":"HCP anatomy to use as template for EEG dataset",                "base_path":"/mnt/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/ciftify-ICBM152",                "template_name":"ICBM152",                "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/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/fsl_bet-ICBM152"        },        "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":"template",        "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/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/ciftify",                "T1w_file_name":"T1w.nii.gz",                "Atlas_file_name":"aparc.a2009s+aseg.nii.gz"            },{                "id":"template",                "name":"hcp_anat_template",                "description":"HCP anatomy to use as template for EEG dataset",                "base_path":"/mnt/Data/Talia/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/Data/Talia/MIITRA/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        }    }}
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		@@ -1 +1 @@
		{ "description":"", "modality":"EEG", "dataset":{ "Name":"CHBMP", "Description":"ICBM152" }, "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/Data/Data_report/Test", "tmp_path":"local"}
		{ "description":"", "modality":"EEG", "dataset":{ "Name":"CHBMP", "Description":"ICBM152" }, "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/Data/Talia/MIITRA", "tmp_path":"local"}
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Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{ "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/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/ciftify", "T1w_file_name":"T1w.nii.gz", "Atlas_file_name":"aparc.a2009s+aseg.nii.gz" },{ "id":"template", "name":"hcp_anat_template", "description":"HCP anatomy to use as template for EEG dataset", "base_path":"/mnt/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/ciftify-ICBM152", "template_name":"ICBM152", "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/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/fsl_bet-ICBM152" }, "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":"template", "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/Data/Data_report/CHBMP_EEG_and_MRI/ds_bids_cbm_loris_24_11_21/derivatives/ciftify", "T1w_file_name":"T1w.nii.gz", "Atlas_file_name":"aparc.a2009s+aseg.nii.gz" },{ "id":"template", "name":"hcp_anat_template", "description":"HCP anatomy to use as template for EEG dataset", "base_path":"/mnt/Data/Talia/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/Data/Talia/MIITRA/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 } }}
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