Hopefully fixes imageempty error.

Author: andreashorn

ea_anatpreprocess.m

@@ -0,0 +1,18 @@
+function ea_anatpreprocess(fpth)
+[pth,fn,ext]=fileparts(fpth);
+copyfile(fpth,fullfile(pth,['k',fn,ext]));
+ea_dcm2nii(fpth);
+
+V=ea_open_vol(fpth);
+if any(V.dim<20)
+    ea_warning('DCM2NII based autocrop and -reorient failed. Continuing without.');
+    copyfile(fullfile(pth,['k',fn,ext]),fpth);
+end
+ea_bias_field_correction(fpth)
+V=ea_open_vol(fpth);
+if any(V.dim<20)
+    ea_warning('Biasfield correction failed. Continuing without.');
+    copyfile(fullfile(pth,['k',fn,ext]),fpth);
+end
+delete(['k',fn,ext]);
+

ea_assignpretra.m

@@ -19,8 +19,7 @@
 if ~exist([directory,'.pp'],'file') && ~exist([directory,'ea_normmethod_applied.mat'],'file') % only do this once, small hidden flag .pp inside patient folder will show this has been done before.
     for fi=f
         % apply biasfieldcorrection and reorient/crop
-        ea_dcm2nii([directory,options.prefs.rawpreniis{fi}]);
-        ea_bias_field_correction([directory,options.prefs.rawpreniis{fi}])
+        ea_anatpreprocess([directory,options.prefs.rawpreniis{fi}]);
     end
     try
     fs=fopen([directory,'.pp'],'w');

ea_coreg_all_mri.m

@@ -39,8 +39,7 @@
     if exist([directory,options.prefs.prenii_unnormalized_t1],'file')
         disp('Including T1 data for (grey-matter) normalization');
         if ~includeatlas
-%        ea_dcm2nii([directory,options.prefs.prenii_unnormalized_t1]);
-%        ea_bias_field_correction([directory,options.prefs.prenii_unnormalized_t1])
+
         ea_coreg2images(options,[directory,options.prefs.prenii_unnormalized_t1],[directory,options.prefs.prenii_unnormalized],[directory,options.prefs.prenii_unnormalized_t1]);
         end
         to{cnt}=[options.earoot,'templates',filesep,'mni_hires_t1.nii'];
@@ -59,7 +58,6 @@
     if exist([directory,options.prefs.prenii_unnormalized_pd],'file')
         disp('Including PD data for (grey-matter) normalization');
         if ~includeatlas
-%        ea_dcm2nii([directory,options.prefs.prenii_unnormalized_pd]);
         ea_coreg2images(options,[directory,options.prefs.prenii_unnormalized_pd],[directory,options.prefs.prenii_unnormalized],[directory,options.prefs.prenii_unnormalized_pd]);
         end
         to{cnt}=[options.earoot,'templates',filesep,'mni_hires_pd.nii'];