Zeffiro developer: A regular push adding the changes made in the curr…

…ent local repository to the remote origin. Contents of the folders ./data/ and ./profile/ are ignored. The update necessitates creating a personal access token.

m/lead_field/zef_lead_field_matrix.m

@@ -265,7 +265,7 @@
 end
 
 if zef.source_interpolation_on
-    zef_source_interpolation;
+    zef = zef_source_interpolation(zef);
 end
 
 if nargout == 0

m/zef_transfer_matrix.m

@@ -238,9 +238,16 @@
 
         % Define block size
 
-        delete(gcp('nocreate'))
         parallel_processes = eval( 'zef.parallel_processes');
-        parpool(parallel_processes);
+         if isempty(gcp('nocreate'))
+            parpool(n_parallel);
+  else
+      h_pool = gcp;
+      if not(isequal(h_pool.NumWorkers,parallel_processes))
+          delete(h_pool)
+          parpool(parallel_processes);
+      end
+    end
         processes_per_core = eval( 'zef.processes_per_core');
         tic;
         block_size =  parallel_processes*processes_per_core;

scripts/inverse_sensitivity/zef_run_sensitivity_maps.m

@@ -1,3 +1,29 @@
-project_struct = zeffiro_interface('start_mode','nodisplay','open_project','data/example_projects/ary_sphere_project_2');
+%This script calculates averaged sensitivity maps using the MNE and dipole
+%scan tools. Start the script from the root folder by first adding the
+%script folder into the path (addpath('scripts/inverse_sensitivity')).
+
+%Import the spherical Ary domain.
+project_struct = zeffiro_interface('start_mode','nodisplay','open_project','data/example_projects/ary_sphere_project');
+
+%Set mesh resolution and generate a finite element mesh.
+project_struct.mesh_resolution = 6;
+project_struct = zef_create_finite_element_mesh(project_struct);
+
+%Set the desired number of source positions and generate a lead field.
+project_struct.n_sources = 500;
+project_struct = zef_eeg_lead_field(project_struct);
+
+%Set noise level and number of cases to be averaged.
+noise_level = -30;
+n_cases = 2;
+
+%Start the MNE tool and calculate a map for sLORETA.
+project_struct = zef_minimum_norm_estimation(project_struct);
+sensitivity_map_sLoreta = zef_sensitivity_map_mne(project_struct, 'sLORETA', n_cases, noise_level);
+
+%Start the dipole scan tool and calculate a map. 
 project_struct = zef_dipole_start(project_struct);
-sensitivity_map = zef_sensitivity_map_dipoleScan(project_struct, 2, -30)
+sensitivity_map_dipoleScan = zef_sensitivity_map_dipoleScan(project_struct, n_cases, noise_level);
+
+%Close Zeffiro.
+zef_close_all;

scripts/inverse_sensitivity/zef_sensitivity_map_dipoleScan.m

@@ -22,6 +22,10 @@
 hauk_map.angle_vec_avg = zeros(size(hauk_map.angle_vec{1}));
 hauk_map.mag_vec_avg = zeros(size(hauk_map.mag_vec{1}));
 
+hauk_map.dist_vec_std = zeros(size(hauk_map.dist_vec{1}));
+hauk_map.angle_vec_std = zeros(size(hauk_map.angle_vec{1}));
+hauk_map.mag_vec_std = zeros(size(hauk_map.mag_vec{1}));
+
 for i = 1 : n_reconstructions
 hauk_map.dist_vec_avg = hauk_map.dist_vec_avg + hauk_map.dist_vec{i};
 hauk_map.angle_vec_avg = hauk_map.angle_vec_avg + hauk_map.angle_vec{i};
@@ -32,5 +36,15 @@
 hauk_map.angle_vec_avg = hauk_map.angle_vec_avg/n_reconstructions;
 hauk_map.mag_vec_avg = hauk_map.mag_vec_avg/n_reconstructions;
 
+for i = 1 : n_reconstructions
+hauk_map.dist_vec_std = hauk_map.dist_vec_std + (hauk_map.dist_vec{i} - hauk_map.dist_vec_avg).^2;
+hauk_map.angle_vec_std = hauk_map.angle_vec_std + (hauk_map.angle_vec{i} - hauk_map.angle_vec_avg).^2;
+hauk_map.mag_vec_std = hauk_map.mag_vec_std + (hauk_map.mag_vec{i} - hauk_map.mag_vec_avg).^2;
+end
+
+hauk_map.dist_vec_std = sqrt(hauk_map.dist_vec_std/(n_reconstructions-1));
+hauk_map.angle_vec_std = sqrt(hauk_map.angle_vec_std/(n_reconstructions-1));
+hauk_map.mag_vec_std = sqrt(hauk_map.mag_vec_std/(n_reconstructions-1));
+
 
 end

scripts/inverse_sensitivity/zef_sensitivity_map_mne.m

@@ -8,7 +8,7 @@
   end
 
   weighting_type_cell = {'mne','dspm','sloreta'};
-  weighting_type = find(ismember(weighting_type_cell,weighting_type));
+  weighting_type = find(ismember(weighting_type_cell,lower(weighting_type)));
 
 sensitivity_map = struct;
 sensitivity_map.weighting_type = weighting_type_cell{weighting_type}; 

scripts/zef_KalmanDemo.m

@@ -2,7 +2,7 @@ function KalmanDemo()
 % How to use kalman without GUI
 
 % Create project
-project_struct = zef_
+project_struct = zeffiro_interface('start_mode','nodisplay','import_to_new_project','scripts/scripts_for_importing/multicompartment_head_project/import_segmentation.zef');
 
 % Set mesh resolution
 project_struct.mesh_resolution = 4.5;