Moved biasfieldcorrection and crop/reorient to begin of Lead-Pipeline.

ea_assignpretra.m

@@ -13,6 +13,17 @@
 if isempty(f)
     ea_error(['No anatomy information found. Please put either ',options.prefs.rawpreniis{1},', ',  options.prefs.rawpreniis{2},' or ', options.prefs.rawpreniis{3}, ' into subject folder.']);
 end
+
+
+if ~exist([directory,'.pp'],'file') % only do this once, small hidden flag .pp inside patient folder will show this has been done before.
+for f=find(fexist)
+% apply biasfieldcorrection and reorient/crop
+    ea_dcm2nii([directory,options.prefs.rawpreniis{f}]);
+    ea_bias_field_correction([directory,options.prefs.rawpreniis{f}]) 
+end
+fs=fopen([directory,'.pp'],'w');
+end
+
 options.prefs.prenii_unnormalized=options.prefs.rawpreniis{f(1)};
 options.primarytemplate=ptemps{f(1)};
 

ea_normalize_ants_multimodal.m

@@ -39,9 +39,7 @@
     bprfx='';
 end
 
-ea_dcm2nii([directory,options.prefs.prenii_unnormalized]);
-ea_bias_field_correction([directory,options.prefs.prenii_unnormalized])
-
+
 % T1
 if uset1 && ~strcmp(options.primarytemplate,'_t1')
     if exist([directory,options.prefs.prenii_unnormalized_t1],'file')