Allow to build upon preexisting ANTs warps.

ea_normsettings_ants.m

@@ -22,7 +22,7 @@
 
 % Edit the above text to modify the response to help ea_normsettings_ants
 
-% Last Modified by GUIDE v2.5 02-Dec-2018 14:34:00
+% Last Modified by GUIDE v2.5 29-Dec-2018 11:48:39
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -114,6 +114,9 @@ function ea_normsettings_ants_OpeningFcn(hObject, eventdata, handles, varargin)
 
 set(handles.skullstripped,'Value',prefs.machine.normsettings.ants_skullstripped);
 
+set(handles.usepreexisting,'Value',prefs.machine.normsettings.ants_usepreexisting);
+
+
 % UIWAIT makes ea_normsettings_ants wait for user response (see UIRESUME)
 
 
@@ -179,6 +182,8 @@ function savebutn_Callback(hObject, eventdata, handles)
 
 normsettings.ants_reinforcetargets=get(handles.reinforcetargets,'Value');
 
+normsettings.ants_usepreexisting=get(handles.usepreexisting,'Value');
+
 
 if get(handles.restrcores,'Value')
     normsettings.ants_numcores=get(handles.numcores,'String');
@@ -317,3 +322,26 @@ function reinforcetargets_Callback(hObject, eventdata, handles)
 % handles    structure with handles and user data (see GUIDATA)
 
 % Hint: get(hObject,'Value') returns toggle state of reinforcetargets
+
+
+% --- Executes on selection change in usepreexisting.
+function usepreexisting_Callback(hObject, eventdata, handles)
+% hObject    handle to usepreexisting (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = cellstr(get(hObject,'String')) returns usepreexisting contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from usepreexisting
+
+
+% --- Executes during object creation, after setting all properties.
+function usepreexisting_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to usepreexisting (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: popupmenu controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end

ext_libs/ANTs/ea_ants_nonlinear.m

@@ -194,8 +194,7 @@ function ea_ants_nonlinear(varargin)
 end
 
 
-rigidstage = [' --initial-moving-transform [', fixedimage{1}, ',', movingimage{1}, ',0]' ...
-    ' --transform Rigid[0.25]' ... % bit faster gradient step (see https://github.com/stnava/ANTs/wiki/Anatomy-of-an-antsRegistration-call)
+rigidstage = [' --transform Rigid[0.25]' ... % bit faster gradient step (see https://github.com/stnava/ANTs/wiki/Anatomy-of-an-antsRegistration-call)
     ' --convergence ', rigidconvergence, ...
     ' --shrink-factors ', rigidshrinkfactors, ...
     ' --smoothing-sigmas ', rigidsmoothingssigmas, ...
@@ -289,6 +288,8 @@ function ea_ants_nonlinear(varargin)
     setenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS',options.prefs.machine.normsettings.ants_numcores) % no num2str needed since stored as string.
 end
 
+props.moving = movingimage{1};
+props.fixed = fixedimage{1};
 props.outputbase = outputbase;
 props.ANTS = ANTS;
 props.outputimage = outputimage;
@@ -299,12 +300,12 @@ function ea_ants_nonlinear(varargin)
 props.synmaskstage = synmaskstage;
 props.directory = directory;
 props.stagesep = options.prefs.machine.normsettings.ants_stagesep;
-if exist([fileparts(movingimage{1}),filesep,'glanatComposite.h5'],'file')
-    % clean old deformation field. this is important for cases where ANTs
-    % crashes and the user does not get an error back. Then, preexistant old transforms
-    % will be considered as new ones.
-    delete([fileparts(movingimage{1}),filesep,'glanatComposite.h5']);
-end
+% if exist([fileparts(movingimage{1}),filesep,'glanatComposite.h5'],'file')
+%     % clean old deformation field. this is important for cases where ANTs
+%     % crashes and the user does not get an error back. Then, preexistant old transforms
+%     % will be considered as new ones.
+%     delete([fileparts(movingimage{1}),filesep,'glanatComposite.h5']);
+% end
 ea_submit_ants_nonlinear(props);
 
 if exist('tmaskdir','var')

ext_libs/ANTs/ea_submit_ants_nonlinear.m

@@ -8,6 +8,34 @@ function ea_submit_ants_nonlinear(props)
 
 
 function ea_antsnl_monostep(props)
+directory=fileparts(props.moving);
+directory=[directory,filesep];
+if exist([fileparts(props.moving),filesep,'glanatComposite',ea_getantstransformext(directory)],'file') % prior ANTs transform found.
+    prefs=ea_prefs;
+    switch prefs.machine.normsettings.ants_usepreexisting
+        case 1 % ask
+            answ=questdlg('We found an old ANTs transform file. Do you wish to reuse the transform or discard the old one?','Old ANTs transform found.','Reuse','Discard','Discard');
+            switch lower(answ)
+                case 'reuse'
+                    initreg=[' --initial-moving-transform ',ea_path_helper([fileparts(props.moving),filesep,'glanatComposite',ea_getantstransformext(directory)])];
+                    props.rigidstage='';
+                    props.affinestage='';
+                case 'discard'
+                    ea_delete([fileparts(props.moving),filesep,'glanatComposite',ea_getantstransformext(directory)])
+                    initreg=[' --initial-moving-transform [', props.fixed, ',', props.moving, ',0]'];
+            end
+        case 2 % reuse
+            initreg=[' --initial-moving-transform ',ea_path_helper([fileparts(props.moving),filesep,'glanatComposite',ea_getantstransformext(directory)])];
+            props.rigidstage='';
+            props.affinestage='';
+        case 3 % overwrite
+            % clean old deformation field. this is important for cases where ANTs
+            % crashes and the user does not get an error back. Then, preexistant old transforms
+            % will be considered as new ones.
+            ea_delete([fileparts(props.moving),filesep,'glanatComposite',ea_getantstransformext(directory)])
+            initreg=[' --initial-moving-transform [', props.fixed, ',', props.moving, ',0]']; 
+    end
+end
 
 cmd = [props.ANTS, ' --verbose 1', ...
     ' --dimensionality 3', ...
@@ -17,6 +45,7 @@ function ea_antsnl_monostep(props)
     ' --float 1',...
     ' --winsorize-image-intensities [0.005,0.995]', ...
     ' --write-composite-transform 1', ...
+    initreg, ...
     props.rigidstage, props.affinestage, props.synstage, props.slabstage, props.synmaskstage];
 
 fid = fopen([props.directory,'ea_ants_command.txt'],'a');