Can now generate checkregfiles from Menu, too

ea_autocoord.m

@@ -94,6 +94,12 @@ function ea_autocoord(options)
         ea_gencoregcheckfigs(options); % generate checkreg figures
     end
 
+    if isfield(options,'gencheckreg') % this case is an exception when calling from the Tools menu.
+        if options.gencheckreg
+                    ea_gencoregcheckfigs(options); % generate checkreg figures
+        end
+    end
+
     if options.dolc % perform lead connectome subroutine..
         ea_perform_lc(options);
     end

ea_gencheckreg.m

@@ -0,0 +1,17 @@
+function ea_gencheckreg(~,~,handles)
+% function to simply export checkreg figures for selected patients from
+% Menu
+
+disp('Generating check-reg figures for selected patients...');
+leadfigure=handles.leadfigure;
+ea_busyaction('on',leadfigure,'dbs');
+
+
+options=ea_handles2options(handles);
+options.macaquemodus=getappdata(handles.leadfigure,'macaquemodus');
+
+options.uipatdirs=getappdata(handles.leadfigure,'uipatdir');
+options.gencheckreg=1;
+ea_run('run',options);
+
+ea_busyaction('off',leadfigure,'dbs');

ea_gencoregcheckfigs.m

@@ -24,10 +24,11 @@ function ea_gencoregcheckfigs(options)
             [directory,options.prefs.gcornii],...
             [directory,options.prefs.gsagnii]};
     case 2
-        ea_tonemapct_file(options);
+        ea_tonemapct_file(options,'native');
+        ea_tonemapct_file(options,'mni');
         fis2anat={[directory,'tp_',options.prefs.ctnii_coregistered]};
         fis2mni={[directory,options.prefs.gprenii],...
-            [directory,options.prefs.gctnii]};
+            [directory,'tp_',options.prefs.gctnii]};
 end
 fis2anat=[fis2anat,oanat'];
 

ea_genvat_simbio_iso2mesh.m

@@ -337,7 +337,10 @@
         spacing(dim)=abs(gv{dim}(1)-gv{dim}(2));
     end
 catch
-    keyboard % vat empty..!
+varargout{1}=nan;
+varargout{2}=nan;
+varargout{3}=nan;
+return
 end
 
 ea_dispt('Creating nifti header for export...');
@@ -413,20 +416,20 @@
 save(stimfile,'S');
 %spm_write_vol(Vvat,flipdim(eg,3));
 
-Vvate.img=permute(eeg,[2,1,3]);
+Vvate.img=eeg; %permute(eeg,[2,1,3]);
 ea_write_nii(Vvate);
 
-Vvatne.img=permute(neeg,[2,1,3]);
+Vvatne.img=neeg; %permute(neeg,[2,1,3]);
 ea_write_nii(Vvatne);
 
-Vvat.img=permute(eg,[2,1,3]);
+Vvat.img=eg; %permute(eg,[1,2,3]);
 ea_write_nii(Vvat);
 
 
 ea_dispt('Calculating isosurface to display...');
-vatfv=isosurface(xg,yg,zg,Vvat.img,0.75);
+vatfv=isosurface(xg,yg,zg,permute(Vvat.img,[2,1,3]),0.75);
 
-caps=isocaps(xg,yg,zg,Vvat.img,0.5);
+caps=isocaps(xg,yg,zg,permute(Vvat.img,[2,1,3]),0.5);
 
 vatfv.faces=[vatfv.faces;caps.faces+size(vatfv.vertices,1)];
 vatfv.vertices=[vatfv.vertices;caps.vertices];

ea_showfibres_volume.m

@@ -104,7 +104,13 @@
 
 
         if ~exist('K','var') % e.g. maedler model used
-            K(side).K{vat}=convhulln(VAT{side}.VAT{vat}+randn(size(VAT{side}.VAT{vat}))*0.000001); % create triangulation.
+            try
+                K(side).K{vat}=convhulln(VAT{side}.VAT{vat}+randn(size(VAT{side}.VAT{vat}))*0.000001); % create triangulation.
+            catch
+                if isnan(VAT{side}.VAT) % empty VTA
+                    continue
+                end
+            end
         else % still maedler model used
             try
                 K(side).K{vat}; % not defined

ea_tonemapct_file.m

@@ -1,10 +1,21 @@
-function ea_tonemapct_file(options)
+function ea_tonemapct_file(options,nativemni)
 ea_dispt('Tonemapping CT...');
-directory=[options.root,options.patientname,filesep];
-ct=ea_load_nii([directory,options.prefs.ctnii_coregistered]);
-ct.fname=[directory,'tp_',options.prefs.ctnii_coregistered];
-
-ct.img=ea_tonemap_ct(ct.img);
-ea_write_nii(ct);
+if ~exist('nativemni','var')
+    nativemni='native';
+end
+switch nativemni
+    case 'native'
+        directory=[options.root,options.patientname,filesep];
+        ct=ea_load_nii([directory,options.prefs.ctnii_coregistered]);
+        ct.fname=[directory,'tp_',options.prefs.ctnii_coregistered];        
+        ct.img=ea_tonemap_ct(ct.img);
+        ea_write_nii(ct);
+    case 'mni'
+        directory=[options.root,options.patientname,filesep];
+        ct=ea_load_nii([directory,options.prefs.gctnii]);
+        ct.fname=[directory,'tp_',options.prefs.gctnii];
+        ct.img=ea_tonemap_ct(ct.img);
+        ea_write_nii(ct);
+end
 
 ea_dispt('');

helpers/gui/ea_menu_initmenu.m

@@ -25,6 +25,10 @@ function ea_menu_initmenu(handles,cmd)
         ea_menu_addsubmit(handles);
     end
 
+    if ismember('checkregfigs',cmd)
+       uimenu(f,'Label','Generate Checkreg figures','Callback',{@ea_gencheckreg,handles}); 
+    end
+
     if ismember('transfer',cmd)
        ea_menu_addtransfer(handles,callingfunction); 
     end

lead_dbs.m

@@ -189,7 +189,7 @@ function lead_dbs_OpeningFcn(hObject, eventdata, handles, varargin)
 
 
 %% add tools menu
-ea_menu_initmenu(handles,{'acpc','export','cluster','prefs','vatcon','transfer'});
+ea_menu_initmenu(handles,{'acpc','export','cluster','prefs','vatcon','transfer','checkregfigs'});