Update example.m

example.m

@@ -4,30 +4,23 @@
 % clear all; %close all;
 
 dir_fastfield='/Users/mehri.baniasadi/Documents/GitHub/FastField';
-dir_patient = '/Users/mehri.baniasadi/Desktop/SelectedPatients/BOSTON/96376/DistalPacer96376/output/dbsar2leaddbs';
-dir_patient = pwd;
+dir_patient = '/Users/mehri.baniasadi/Documents/GitHub/FastField/case_studies/case_study_1';
+
 % Perc is the percentage assigned to each contact
 % for segmented electrodes
 % 1 is is the bottom contact, 8 is the topest contact
 % 2,3,4 are each segment of the second ring from the bottom
 % 5,6,7 are each segment of the third ring from the bottom
 % for ring elecetrodes 
 % 1 is the bottom contact then 2 and 3,and 4 the topeset contact;
-%
-perc = [0 15 75 10 0 0 0 0];
-%perc = [0 32 0 0 68 0 0 0];
-%perc=[40 60 0 0 0 0 0 0];
-%perc=[0 24 23 23 10 10 10 0]
-%perc=[0 25 0 25 25 0 25 0];
-%perc=[0 0 0 100];
-%perc=[0 55 45 0]
-%perc=[60 40 0 0]
-%amp = 2.5; % amplitude in mA
-amp=3;
-side = 2; % Right is 1,  Left is 2
-
-Electrode_type = 'boston_vercise'; %'medtronic_3389'; % 'boston_vercise';'medtronic_3387';
+perc = [50 50 0 0 0 0 0 0];
+
+amp=2.2;
+side = 1; % Right is 1,  Left is 2
+
+Electrode_type = 'boston_vercise_directed'; %'medtronic_3389'; % 'boston_vercise';'medtronic_3387';
 %  Electrode_type = 'pins_l303'   % 'boston_vercise_directed';
+
   %'stjude_directed_short'; %'stjude_directed_long';  
                                              %'stjude_activetip_2mm'; 'stjude_activetip_3mm'
 conductivity = 0.1;
@@ -47,68 +40,16 @@
 % get the Efield
 [Efield,xg,yg,zg,elfv,trans_mat] = fastfield_main(standard_efield,grid_vec,electrode,electrode_patient,perc,amp,side,conductivity,amp_mode);
 
-% brain_structures{1} = 'STN1';
+brain_structures{1} = 'GPi2';
 
 % for t=1:length(atlases.labels{1, 1})
 %  brain_structures{t} =   atlases.labels{1, 1}{t};
 % end
 
-% visualize Efield
-% 
+
 figure;
 hold on;
 
 plot_elec(elfv,electrode,perc);
 plot_efield(Efield,xg,yg,zg,plot_choice,Threshold);
 
-%plot_atlas(brain_structures,atlases,side) 
-
-%view(180,0)
-%camlight('left');
-%camlight( 90, -45, 'infinite');
-%camlight( 90, 45, 'infinite');
-
-
-
-%%
-hold on;
-
-    cut = 1:100;
-
-    data = Efield(:,:,cut);
-    X=xg;
-    Y=yg;
-    Z=zg;
-
-    cmap = colormap(autumn);
-    hGroupField = hggroup();
-    h = {};
-
-
-    s = isosurface(X(:,:,cut), Y(:,:,cut), Z(:,:,cut), data > Threshold );
-
-    h{end+1} = patch(s, 'EdgeColor', 'none', 'FaceColor', [0.8 0.2 0.2] , 'FaceAlpha', 0.3, 'Parent', hGroupField);
-
-
-
-conductivity = 0.22;
-
-[Efield,xg,yg,zg,elfv,trans_mat] = fastfield_main(standard_efield,grid_vec,electrode,electrode_patient,perc,amp,side,conductivity,amp_mode);
-hold on;
-
-    cut = 1:100;
-
-    data = Efield(:,:,cut);
-    X=xg;
-    Y=yg;
-    Z=zg;
-
-    cmap = colormap(autumn);
-    hGroupField = hggroup();
-    h = {};
-
-
-    s = isosurface(X(:,:,cut), Y(:,:,cut), Z(:,:,cut), data > Threshold );
-
-    h{end+1} = patch(s, 'EdgeColor', 'none', 'FaceColor', [0.2 0.2 0.8] , 'FaceAlpha', 0.3, 'Parent', hGroupField);
-