Further additions to refine structures pipeline.

gmilab · Jan 25, 2019 · 8fb99be · 8fb99be
1 parent b1f78e4
commit 8fb99be
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Showing 6 changed files with 34 additions and 1 deletion.
diff --git a/ea_autocoord.m b/ea_autocoord.m
@@ -209,6 +209,10 @@ function ea_autocoord(options)
             ea_subcorticalrefine(options);
         end
     end
+
+    if options.normalize.refine
+       ea_checkstructures(options); 
+    end
 
 if options.ecog.extractsurface.do
    switch options.ecog.extractsurface.method

diff --git a/ea_checkcoreg.fig b/ea_checkcoreg.fig
diff --git a/ea_checkstructures.m b/ea_checkstructures.m
@@ -627,7 +627,10 @@ function checkstructures_CloseRequestFcn(hObject, eventdata, handles)
 % Hint: delete(hObject) closes the figure
 uuid=getappdata(handles.checkstructures,'fidguiid');
 if ~isempty(uuid)
+
+
     disp('Adding corrections to fiducial markers...');
+    disp('Remember that changes only take effect if you rerun ANTs-based normalization!');
 
     options=getappdata(handles.checkstructures,'options');
     cexpmm=getappdata(handles.checkstructures,'allcexpmm');
@@ -697,6 +700,18 @@ function checkstructures_CloseRequestFcn(hObject, eventdata, handles)
         delete(fullfile(pathn,filen));
     end
     disp('Done.');
+
+    % unapprove normalization since should be redone:
+    directory=[options.root,options.patientname,filesep];
+    approved=load([directory,'ea_coreg_approved.mat']);
+    approved.(ea_stripex(options.prefs.gprenii))=0;
+    save([directory,'ea_coreg_approved.mat'],'-struct','approved');
+
+    if strcmp(computer('arch'),'maci64')
+        system(['xattr -wx com.apple.FinderInfo "0000000000000000000C00000000000000000000000000000000000000000000" ',ea_path_helper([directory,ea_stripex(options.prefs.gprenii),'.nii'])]);
+    end
+
+
 else
         delete(hObject);
 end
diff --git a/ea_handles2options.m b/ea_handles2options.m
@@ -52,6 +52,11 @@
     end
 end
 
+options.normalize.refine=0;
+try
+    options.normalize.refine=get(handles.refinefit,'Value');
+end
+
 try % not working when calling from lead_anatomy
     options.coregmr.check=(get(handles.coregmrcheck,'Value') == get(handles.coregmrcheck,'Max'));
 catch

diff --git a/lead_dbs.fig b/lead_dbs.fig
diff --git a/lead_dbs.m b/lead_dbs.m
@@ -22,7 +22,7 @@
 
 % Edit the above text to modify the response to help lead_dbs
 
-% Last Modified by GUIDE v2.5 01-Oct-2018 10:34:41
+% Last Modified by GUIDE v2.5 25-Jan-2019 09:22:24
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -1902,3 +1902,12 @@ function surfacemethod_CreateFcn(hObject, eventdata, handles)
 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
     set(hObject,'BackgroundColor','white');
 end
+
+
+% --- Executes on button press in refinefit.
+function refinefit_Callback(hObject, eventdata, handles)
+% hObject    handle to refinefit (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of refinefit