Fixed error reported by S.magothr. (New Segment error).

ea_checkforwardinv.m

@@ -0,0 +1,18 @@
+function ea_checkforwardinv(options,forwardinv)
+
+switch forwardinv
+    case 'forward'
+        V=spm_vol([options.root,options.patientname,filesep,'y_ea_normparams.nii']);
+        Vmni=spm_vol([options.earoot,'templates',filesep,'mni_hires.nii']);
+
+        if ~isequal(V.dim,Vmni.dim)
+
+            ea_redo_inv([options.root,options.patientname,filesep],options,'forward');
+        end
+    case 'inverse'
+        V=spm_vol([options.root,options.patientname,filesep,'y_ea_inv_normparams.nii']);
+        Vanat=spm_vol([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized]);
+        if ~isequal(V.dim,Vanat.dim)
+            ea_redo_inv([options.root,options.patientname,filesep],options,'inverse');
+        end
+end

ea_generate_tpm.m

@@ -1,13 +1,45 @@
-function ea_generate_tpm
+function ea_generate_tpm(varargin)
 
 spmdir=[fileparts(which('spm')),filesep];
 earoot=[fileparts(which('lead')),filesep];
+if nargin
+    earoot=varargin{1}.earoot;
+end
 
 switch spm('ver')
     case 'SPM8'
-copyfile([spmdir,'toolbox',filesep,'Seg',filesep,'TPM.nii'],[earoot,'templates',filesep,'TPM.nii']);
+        copyfile([spmdir,'toolbox',filesep,'Seg',filesep,'TPM.nii'],[earoot,'templates',filesep,'TPM.nii']);
     case 'SPM12'
-copyfile([spmdir,'tpm',filesep,'TPM.nii'],[earoot,'templates',filesep,'TPM.nii']);
+        copyfile([spmdir,'tpm',filesep,'TPM.nii'],[earoot,'templates',filesep,'TPM.nii']);
 end
 
-ea_reslice_nii([earoot,'templates',filesep,'TPM.nii'],[earoot,'templates',filesep,'TPM.nii'],[0.5 0.5 0.5],0,0,3);
+
+for tp=1:6
+    matlabbatch{1}.spm.util.imcalc.input = {[earoot,'templates',filesep,'mni_hires.nii']
+        [earoot,'templates',filesep,'TPM.nii,1']
+        [earoot,'templates',filesep,'TPM.nii,2']
+        [earoot,'templates',filesep,'TPM.nii,3']
+        [earoot,'templates',filesep,'TPM.nii,4']
+        [earoot,'templates',filesep,'TPM.nii,5']
+        [earoot,'templates',filesep,'TPM.nii,6']};
+    matlabbatch{1}.spm.util.imcalc.output = [earoot,'templates',filesep,'TPM_',num2str(tp),'.nii'];
+    matlabbatch{1}.spm.util.imcalc.outdir = {''};
+    matlabbatch{1}.spm.util.imcalc.expression = ['i',num2str(tp+1)];
+    matlabbatch{1}.spm.util.imcalc.var = struct('name', {}, 'value', {});
+    matlabbatch{1}.spm.util.imcalc.options.dmtx = 0;
+    matlabbatch{1}.spm.util.imcalc.options.mask = 0;
+    matlabbatch{1}.spm.util.imcalc.options.interp = 1;
+    matlabbatch{1}.spm.util.imcalc.options.dtype = 4;
+    cfg_util('run',{matlabbatch});
+    fis{tp}=[earoot,'templates',filesep,'TPM_',num2str(tp),'.nii'];
+end
+clear matlabbatch
+matlabbatch{1}.spm.util.cat.vols = fis;
+matlabbatch{1}.spm.util.cat.name = [earoot,'templates',filesep,'TPM.nii'];
+matlabbatch{1}.spm.util.cat.dtype = 4;
+cfg_util('run',{matlabbatch});
+
+for fi=1:length(fis)
+    delete(fis{fi});
+end
+delete([earoot,'templates',filesep,'TPM.mat']);

ea_map_coords.m

@@ -176,6 +176,7 @@
 Vx=spm_vol([hdwim,',1,1']);
 Vy=spm_vol([hdwim,',1,2']);
 Vz=spm_vol([hdwim,',1,3']);
+
 for i = 1:size(coord, 2)
     ind = inds(:, i);
     coord(1,i)=spm_sample_vol(Vx,ind(1),ind(2),ind(3),1);

ea_reconstruction2native.m

@@ -13,19 +13,19 @@ function ea_reconstruction2native(options)
     [~,tempfile]=ea_whichnormmethod(directory);
     nii=ea_load_nii(tempfile);
 
-
+                ea_checkforwardinv(options,'forward')
+
         for side=options.sides
+
+
             reco.native.coords_mm{side}=ea_warpcoord(reco.mni.coords_mm{side},nii,options);
             reco.native.markers(side).head=ea_warpcoord(reco.mni.markers(side).head,nii,options);
             reco.native.markers(side).tail=ea_warpcoord(reco.mni.markers(side).tail,nii,options);
             reco.native.trajectory{side}=ea_warpcoord(reco.mni.trajectory{side},nii,options);
 
             normtrajvector{side}=mean(diff(reco.native.trajectory{side}))/norm(mean(diff(reco.native.trajectory{side})));
-try
             orth=null(normtrajvector{side})*(options.elspec.lead_diameter/2);
-catch
-    keyboard
-end
+
 
             reco.native.markers(side).x=reco.native.markers(side).head+orth(:,1)';
             reco.native.markers(side).y=reco.native.markers(side).head+orth(:,2)'; % corresponding points in reality

ea_redo_inv.m

@@ -1,6 +1,27 @@
-function ea_redo_inv(directory,options)
-matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.def = {[directory,'y_ea_normparams.nii']};
-matlabbatch{1}.spm.util.defs.comp{1}.inv.space = {[directory,options.prefs.prenii_unnormalized]};
-matlabbatch{1}.spm.util.defs.out{1}.savedef.ofname = 'ea_inv_normparams.nii';
-matlabbatch{1}.spm.util.defs.out{1}.savedef.savedir.saveusr = {directory};
-spm_jobman('run',{matlabbatch});
+function ea_redo_inv(varargin)
+directory=varargin{1};
+options=varargin{2};
+if nargin>2
+    forinv=varargin{3};
+else
+    forinv='inverse';
+end
+switch forinv
+    case 'inverse'
+        matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.def = {[directory,'y_ea_normparams.nii']};
+        matlabbatch{1}.spm.util.defs.comp{1}.inv.space = {[directory,options.prefs.prenii_unnormalized]};
+        matlabbatch{1}.spm.util.defs.out{1}.savedef.ofname = 'ea_inv_normparams.nii';
+        matlabbatch{1}.spm.util.defs.out{1}.savedef.savedir.saveusr = {directory};
+        spm_jobman('run',{matlabbatch});
+
+    case 'forward'
+
+
+        matlabbatch{1}.spm.util.defs.comp{1}.id.space = {[options.earoot,'templates',filesep,'mni_hires.nii']};
+        matlabbatch{1}.spm.util.defs.comp{1}.def = {[directory,'y_ea_normparams.nii']};
+        matlabbatch{1}.spm.util.defs.out{1}.savedef.ofname = 'ea_normparams.nii';
+        matlabbatch{1}.spm.util.defs.out{1}.savedef.savedir.saveusr = {directory};
+        spm_jobman('run',{matlabbatch});
+
+
+end

ext_libs/segment/ea_newseg.m

@@ -1,5 +1,8 @@
 function ea_newseg(directory,file,dartel,options)
 
+if ~exist([options.earoot,'templates',filesep,'TPM.nii'],'file')
+    ea_generate_tpm(options);
+end
 
 disp('Segmentation...');
     switch spm('ver')
@@ -38,7 +41,7 @@ function ea_newseg(directory,file,dartel,options)
             clear matlabbatch
         case 'SPM12'
                 load([options.earoot,'ext_libs',filesep,'segment',filesep,'segjob12']);
-            tpminf=fullfile(fileparts(which('spm')),'tpm',['TPM.nii']);
+            tpminf=[options.earoot,'templates',filesep,'TPM.nii'];
             job.channel.vols{1}=[directory,file,',1'];
             for tpm=1:6
                 job.tissue(tpm).tpm=[tpminf,',',num2str(tpm)];