Added some error messages.

cfg/ea_ui_manualheight.m

@@ -8,7 +8,7 @@ function ea_ui_manualheight(P)
 try
     load([P.foldername{1},'ea_reconstruction']);
 catch
-    error('No reconstruction information found. Please run reconstruction first.');
+    ea_error('No reconstruction information found. Please run reconstruction first.');
 end
 mcfig=figure('name',[patientname,': Manual Height Correction'],'numbertitle','off');
 

ea_autocoord.m

@@ -269,7 +269,7 @@ function ea_autocoord(options)
     try
         load([options.root,patientname,filesep,'ea_reconstruction']);
     catch
-        error('No reconstruction information found. Please run reconstruction first.');
+        ea_error('No reconstruction information found. Please run reconstruction first.');
     end
     mcfig=figure('name',[patientname,': Manual Height Correction'],'numbertitle','off');
     ea_manualcorrection(mcfig,coords_mm,trajectory,patientname,options);

ea_build_DTD.m

@@ -88,6 +88,7 @@
 if isempty(errStr)
     msgStr= sprintf('DTI calculations done, write file dtdStruct as %s',dtdname);
 else
+    ea_error('Error: DTI calculations done, BUT could not write DTD');
     msgStr= sprintf('Error: DTI calculations done, BUT could not write DTD');
 end
 

ea_checkfiles.m

@@ -1,7 +1,7 @@
 function    ea_checkfiles(options)
 % load files
 if strcmp(options.prefs.patientdir,'Choose Patient Directory')
-    error('Please choose patient directory first');
+    ea_error('Please choose patient directory first');
 end
 
 

ea_coreg.m

@@ -14,7 +14,7 @@
         cfundo=[2,1,3,4];
         manual=0;
     otherwise
-        error('Coregistration prefs must be either set to auto or manual. Please modify ea_prefs.m accordingly.');
+        ea_error('Coregistration prefs must be either set to auto or manual. Please modify ea_prefs.m accordingly.');
 end
 
 
@@ -48,7 +48,7 @@
             finas{export}=fina; % assign only if worked.
         catch
             disp('*** Coregistration between transversal and coronar versions failed / Using CT Modality.');
-            %error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+            %ea_error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
         end
         clear matlabbatch jobs;
         if manual
@@ -64,7 +64,7 @@
                     break
                 else
                     if costfun==4
-                        error('Problem cannot be solved automatically.')
+                        ea_error('Problem cannot be solved automatically.')
                     else
                         disp('Trying with another cost-function');
                     end
@@ -106,7 +106,7 @@
         disp('*** Coregistration between pre and post versions worked.');
     catch
         disp('*** Coregistration between pre and post versions failed.');
-        %error('This normalization cannot be performed automatically with LEAD. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+        %ea_error('This normalization cannot be performed automatically with LEAD. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
     end
     clear matlabbatch jobs;
 
@@ -128,7 +128,7 @@
             break
         else
             if costfun==4
-                error('Problem cannot be solved automatically.')
+                ea_error('Problem cannot be solved automatically.')
             else
                 disp('Trying with another cost-function');
             end

ea_error.m

@@ -0,0 +1,8 @@
+function ea_error(msg)
+% The general error message function.
+% __________________________________________________________________________________
+% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
+% Andreas Horn
+
+errordlg(msg);
+error(msg);

ea_ftr2trk.m

@@ -108,7 +108,7 @@ function ea_ftr2trk(ftrfilename,directory,specs,options)
     header = get_header(fid);
 end
 
-if header.hdr_size~=1000, error('Header length is wrong'), end
+if header.hdr_size~=1000, ea_error('FTR-Header length is wrong'), end
 
 % Check orientation
 [tmp ix] = max(abs(header.image_orientation_patient(1:3)));

ea_gencontrastimage.m

@@ -49,7 +49,7 @@
 
 
     otherwise
-        error('Please set Contrast accurately.');
+        ea_error('Please set Contrast accurately.');
 
 end
 

ea_normalize.m

@@ -20,7 +20,7 @@ function ea_normalize(options)
 % Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
 % Andreas Horn
 
-usecombined=0; % if set, eauto will try to fuse coronar and transversal images before normalizing them.
+usecombined=0; % if set, LEAD-DBS will try to fuse coronar and transversal images before normalizing them.
 
 
 if exist([options.root,options.prefs.patientdir,filesep,options.prefs.tranii_unnormalized,'.gz'],'file')
@@ -70,7 +70,7 @@ function ea_normalize(options)
 disp('*** Segmentation of transversal version worked.');
 catch
 disp('*** Segmentation of transversal version failed.');
-error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+ea_error('This normalization cannot be performed automatically with LEAD-DBS. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 
@@ -139,7 +139,7 @@ function ea_normalize(options)
 disp('*** Coregistration between transversal and coronar versions worked.');
 catch
 disp('*** Coregistration between transversal and coronar versions failed.');
-%error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+%ea_error('This normalization cannot be performed automatically with LEAD-DBS. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 
@@ -172,7 +172,7 @@ function ea_normalize(options)
 disp('*** Grand mean normalization (1/3) worked.');
 catch
 disp('*** Grand mean normalization (1/3) failed.');
-error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+ea_error('This normalization cannot be performed automatically with LEAD-DBS. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 

ea_normalize_fibers.m

@@ -3,7 +3,7 @@ function ea_normalize_fibers(options)
 
 [~,preniif]=fileparts(options.prefs.prenii_unnormalized);
 if ~exist([options.root,options.patientname,filesep,'y_ea_inv_normparams.nii'],'file');
-    error('Please run a compatible normalization of the preoperative MRI-volume first. Final (inverse) normalization parameters should be stored as y_ea_inv_normparams.nii inside of the subject folder.');
+    ea_error('Please run a compatible normalization of the preoperative MRI-volume first. Final (inverse) normalization parameters should be stored as y_ea_inv_normparams.nii inside of the subject folder.');
 end
 
 

ea_normalize_schoenecker.m

@@ -90,7 +90,7 @@
     disp('*** Segmentation of transversal version worked.');
 catch
     disp('*** Segmentation of transversal version failed.');
-    error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+    ea_error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 
@@ -159,7 +159,7 @@
     disp('*** Coregistration between transversal and coronar versions worked.');
 catch
     disp('*** Coregistration between transversal and coronar versions failed.');
-    %error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+    %ea_error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 
@@ -192,7 +192,7 @@
     disp('*** Grand mean normalization (1/3) worked.');
 catch
     disp('*** Grand mean normalization (1/3) failed.');
-    error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+    ea_error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 

ea_normalize_schoenecker_pre.m

@@ -169,7 +169,7 @@
 disp('*** Coregistration between preop and postop versions worked.');
 catch
 disp('*** Coregistration between preop and postop versions failed.');
-%error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+%ea_error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 
@@ -202,7 +202,7 @@
 disp('*** Grand mean normalization (1/3) worked.');
 catch
 disp('*** Grand mean normalization (1/3) failed.');
-error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+ea_error('This normalization cannot be performed automatically with eAuto. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 

ea_normalize_spmdartel.m

@@ -173,7 +173,7 @@
     cfg_util('run',jobs);
     disp('*** Dartel coregistration of preoperative version worked.');
 %catch
-%    error('*** Dartel coregistration failed.');
+%    ea_error('*** Dartel coregistration failed.');
 %end
 clear matlabbatch jobs;
 

ea_normalize_spmnewseg.m

@@ -270,7 +270,7 @@ function resize_img(imnames, Voxdim, BB, ismask)
 elseif exist('spm_get','file') % should be true for spm2
     spm5 = 0;
 else
-    error('Can''t find spm_get or spm_select; please add SPM to path')
+    ea_error('Can''t find spm_get or spm_select; please add SPM to path')
 end
 
 spm_defaults;

ea_normalize_spmseg.m

@@ -108,7 +108,7 @@
     disp('*** Segmentation of preoperative version worked.');
 catch
     disp('*** Segmentation of transversal version failed.');
-    error('This normalization cannot be performed automatically with LEAD. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
+    ea_error('This normalization cannot be performed automatically with LEAD. Try using different software for the normalization step. Examples are to use SPM directly, or to use FSL, Slicer or Bioimaging Suite.');
 end
 clear matlabbatch jobs;
 

ea_prepare_slice.m

@@ -72,7 +72,7 @@
    addfactor=addfactor-cnt*0.1;
    ea_showdis(['Lowering initial factor to ',num2str(addfactor),'.'],options.verbose);
     if cnt>500
-        error('Trajectory could not be found. Please choose manual entry-point to select trajectory manually and make sure that images are properly normalized in MNI space.');
+        ea_error('Trajectory could not be found. Please choose manual entry-point to select trajectory manually and make sure that images are properly normalized in MNI space.');
     end
 else
     found=1;

ea_reconstruct_trajectory.m

@@ -247,7 +247,8 @@
 
 
     if round(estpoint(2)-options.maskwindow)<0 || round(estpoint(2)+options.maskwindow)>500 || round(estpoint(1)-options.maskwindow)<0 || round(estpoint(1)+options.maskwindow)>500
-        display('Mask out of bounds. Must have lost trajectory. Try iterating with a different maskwindow again.');
+        close(progressfig)
+        ea_error('Mask out of bounds. Must have lost trajectory. Try iterating with a different maskwindow again.');
 
         return
         %pause

ea_reformat_isomatrix.m

@@ -30,7 +30,7 @@
         stimmat{2}=isom(:,(size(isom,2)/2)+1:end);
 
     else
-        error('Wrong Isomatrix provided.');
+        ea_error('Wrong Isomatrix provided.');
     end
 end
 

ea_render_view.m

@@ -476,7 +476,7 @@ function ea_keyrelease(resultfig,event)
         self.K = [self.K self.K];
     end
     if self.K(1) > 16
-        error('To avoid excessive use of memory, K has been limited to max 16. Change the code to fix this on your own risk.');
+        ea_error('To avoid excessive use of memory, K has been limited to max 16. Change the code to fix this on your own risk.');
     end
     try
         imfilter(zeros(2,2),zeros(2,2));
@@ -498,7 +498,7 @@ function ea_keyrelease(resultfig,event)
         self.aamethod = 'noshrink';
     end
 else
-    error('Wrong syntax, run: help myaa');
+    ea_error('Wrong syntax, run: help myaa');
 end
 
 if length(self.K) == 1

ea_sample_cuboid.m

@@ -167,6 +167,11 @@
 end
 
 
+% error on maxi empty:
+if isempty(maxi)
+    ea_error('Reconstruction failed. Please adjust mask-size and entry-point parameters and re-run reconstruction.');
+end
+
 
 for coo=1:4
     coords(coo,:)=startpt+ntrajvector*maxi       +ntrajvector*(coo*reldist);

ea_savejson.m

@@ -122,7 +122,7 @@
 if(~isempty(jsonopt('FileName','',opt)))
     fid = fopen(opt.FileName, 'wt');
     if ~fid
-        error('No valid destination for lead-server. Read-only filesystem? Please modify prefs.ls.dir in ea_prefs.m to a correct output destination.');
+        ea_error('No valid destination for Lead-server. Read-only filesystem? Please modify prefs.ls.dir in ea_prefs.m to a correct output destination.');
     end
         fwrite(fid,json,'char');
     fclose(fid);
@@ -145,7 +145,7 @@
 function txt=cell2json(name,item,level,varargin)
 txt='';
 if(~iscell(item))
-        error('input is not a cell');
+        ea_error('input is not a cell');
 end
 
 dim=size(item);
@@ -175,7 +175,7 @@
 function txt=struct2json(name,item,level,varargin)
 txt='';
 if(~isstruct(item))
-	error('input is not a struct');
+	ea_error('input is not a struct');
 end
 len=numel(item);
 padding1=repmat(sprintf('\t'),1,level-1);
@@ -212,7 +212,7 @@
 function txt=str2json(name,item,level,varargin)
 txt='';
 if(~ischar(item))
-        error('input is not a string');
+        ea_error('input is not a string');
 end
 item=reshape(item, max(size(item),[1 0]));
 len=size(item,1);
@@ -252,7 +252,7 @@
 %%-------------------------------------------------------------------------
 function txt=mat2json(name,item,level,varargin)
 if(~isnumeric(item) && ~islogical(item))
-        error('input is not an array');
+        ea_error('input is not an array');
 end
 
 padding1=repmat(sprintf('\t'),1,level);
@@ -422,7 +422,7 @@
         opt=setfield(opt,varargin{i},varargin{i+1});
         i=i+1;
     else
-        error('input must be in the form of ...,''name'',value,... pairs or structs');
+        ea_error('input must be in the form of ...,''name'',value,... pairs or structs');
     end
     i=i+1;
 end

ea_showelectrode.m

@@ -148,7 +148,7 @@
         elseif size(options.d3.isomatrix{1},2)==4 % 4 contacts
             shifthalfup=0;
         else
-            error('Isomatrix has wrong size. Please specify a correct matrix.')
+            ea_error('Isomatrix has wrong size. Please specify a correct matrix.')
         end
         end
 

ea_showisovolume.m

@@ -13,7 +13,7 @@ function ea_showisovolume(resultfig,elstruct,options)
 elseif size(options.d3.isomatrix{1},2)==4 % 4 contacts
     shifthalfup=0;
 else
-   error('Isomatrix has wrong size. Please specify a correct matrix.')
+   ea_error('Isomatrix has wrong size. Please specify a correct matrix.')
 end
 for side=options.sides
     cnt=1;

ea_write.m

@@ -5,7 +5,7 @@ function ea_write(options)
     try
         load([options.root,options.patientname,filesep,'ea_reconstruction']);
     catch
-        error('No reconstruction information found. Please run reconstruction first.');
+        ea_error('No reconstruction information found. Please run reconstruction first.');
     end
     for side=1:length(coords_mm)
     if size(coords_mm{side},1)~=options.elspec.numel

ea_writeplanes.m

@@ -283,7 +283,7 @@ function ea_screenshot(outn)
         self.K = [self.K self.K];
     end
     if self.K(1) > 16
-        error('To avoid excessive use of memory, K has been limited to max 16. Change the code to fix this on your own risk.');
+        ea_error('To avoid excessive use of memory, K has been limited to max 16. Change the code to fix this on your own risk.');
     end
     try
         imfilter(zeros(2,2),zeros(2,2));
@@ -305,7 +305,7 @@ function ea_screenshot(outn)
         self.aamethod = 'noshrink';
     end
 else
-    error('Wrong syntax, run: help myaa');
+    ea_error('Wrong syntax, run: help myaa');
 end
 
 if length(self.K) == 1

ext_libs/segment/ea_spm_preproc_run.m

@@ -35,7 +35,7 @@
     case 'vout'
         varargout{1} = vout_job(job);
     otherwise
-        error('Unknown argument ("%s").', arg);
+        ea_error('Unknown argument ("%s").', arg);
 end
 return
 %_______________________________________________________________________
@@ -167,7 +167,7 @@
 
 %_______________________________________________________________________
 function savefields(fnam,p)
-if length(p)>1, error('Can''t save fields.'); end
+if length(p)>1, ea_error('Can''t save fields.'); end
 fn = fieldnames(p);
 if numel(fn)==0, return; end
 for i=1:length(fn)