From 52740bf991d21904ad38c6a8c867ac3b8768fb9d Mon Sep 17 00:00:00 2001
From: Ariosky Areces Gonzalez <48639831+arioskyag@users.noreply.github.com>
Date: Fri, 14 Jun 2024 11:17:30 +0800
Subject: [PATCH] Updating template

---
 cfs_properties/functions/check_properties.m | 21 +++++++++++++++++++--
 cfs_properties/general_params.json          |  2 +-
 cfs_properties/process_import_anat.json     |  2 +-
 3 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/cfs_properties/functions/check_properties.m b/cfs_properties/functions/check_properties.m
index b83e7f7..3fc7ef3 100644
--- 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
index 1b0664c..659fb2b 100644
--- 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"
}
\ No newline at end of file
+{
    "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"
}
\ No newline at end of file
diff --git a/cfs_properties/process_import_anat.json b/cfs_properties/process_import_anat.json
index 850c8c1..ed5d520 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":"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
        }
    }
}
\ 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":"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
        }
    }
}
\ No newline at end of file