Added many bugfixes, as well as DTI tracking functionally (using DTI&…

…Fibertools)
netstim · Feb 7, 2015 · 3cbcbcc · 3cbcbcc
1 parent a510e38
commit 3cbcbcc
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Showing 81 changed files with 2,190 additions and 358 deletions.
diff --git a/.version.txt b/.version.txt
@@ -1,2 +1 @@
- 1.348
- 1.300
+ 1.351
diff --git a/ea_autocoord.m b/ea_autocoord.m
@@ -71,18 +71,46 @@ function ea_autocoord(options)
     try load([options.root,options.patientname,filesep,'ea_coregctmethod_applied']); end
     if exist('coregct_method_applied','var')
         try
-            coregct_method_applied{end+1}=options.normalize.method;
+            coregct_method_applied{end+1}=options.coregct.method;
         catch
-            coregct_method_applied{1}=options.normalize.method;
+            clear coregct_method_applied
+            coregct_method_applied{1}=options.coregct.method;
         end
     else
-        coregct_method_applied{1}=options.normalize.method;
+        coregct_method_applied{1}=options.coregct.method;
     end
     coregct_method_applied=options.coregct.method;
     save([options.root,options.patientname,filesep,'ea_coregctmethod_applied'],'coregct_method_applied');
 end
 
+if options.coregctcheck
+
+
+    % export "control" niftis with wireframe of normal anatomy..
+
+    ea_show_ctcoregistration(options);
+
+end
+
 
+% perform fibertracking
+if options.ft.do
+
+    eval([options.ft.method,'(options)']); % triggers the fibertracking function and passes the options struct to it.
+    try load([options.root,options.patientname,filesep,'ea_ftmethod_applied']); end
+    if exist('ft_method_applied','var')
+        try
+            ft_method_applied{end+1}=options.ft.method;
+        catch
+            clear ft_method_applied
+            ft_method_applied{1}=options.ft.method;
+        end
+    else
+        ft_method_applied{1}=options.ft.method;
+    end
+    ft_method_applied=options.ft.method;
+    save([options.root,options.patientname,filesep,'ea_ftmethod_applied'],'ft_method_applied');
+end
 
 if options.normalize_fibers % normalize fibertracts ? for now these should be denoted in Freiburg format.
     ea_normalize_fibers(options);

diff --git a/ea_build_DTD.m b/ea_build_DTD.m
@@ -1,10 +1,6 @@
 function [mr,b0idx,finames] = ea_build_DTD(bvalue,dirname,dtif,DTDf,HARDIf,bvalf,bvecf)
-
-
-
-
-
-%% filenamen sammeln -> finames
+% converts the dti.nii and dti.bval/.bvec files to Freiburg DTD and raw
+% HARDI-formats.
 
 
 
@@ -22,19 +18,19 @@
 
 
 
-%% hier wird in mrstruct umwandelt
+%% change into mrstruct format
 
 mr =  nifti_to_mrstruct('series3D',finames);
 
 
 sz = size(mr.dataAy);
 
-%% dtd bauen
+%% build dtd
 
-mr.user.bfactor = bvalue; % bwert angeben
+mr.user.bfactor = bvalue; % enter bvalue
 
 
-[mr.user.bDir b0idx] = grads(dirname,bvecf,bvalf); % gradientenrichtungen und b0idxe (siehe unten)
+[mr.user.bDir b0idx] = grads(dirname,bvecf,bvalf); % gradient directions
 
 
 
@@ -45,7 +41,7 @@
 b0_image = mean(mr.dataAy(:,:,:,b0idx),4);
 mean_DTI = mean(mr.dataAy(:,:,:,setdiff(1:sz(4),b0idx)),4);
 
-display('calculating diffusion tensor ...');
+display('Calculating diffusion tensor ...');
 
 Eval = zeros([sz(1:3) 3]);
 Evec = zeros([sz(1:3) 3 3]);
@@ -60,7 +56,7 @@
 
 
 
-display('saving ...');
+display('Done. Saving ...');
 
 
 %% save as dtd_struct
@@ -92,7 +88,7 @@
 if isempty(errStr)
     msgStr= sprintf('DTI calculations done, write file dtdStruct as %s',dtdname);
 else
-    msgStr= sprintf('error: DTI calculations done, BUT could not write DTD');
+    msgStr= sprintf('Error: DTI calculations done, BUT could not write DTD');
 end
 
 % write HARDI

diff --git a/ea_coregctmri_edgedetect.m b/ea_coregctmri_edgedetect.m
@@ -6,37 +6,53 @@
 if ischar(options) % return name of method.
     varargout{1}='Coregister postop-CT with preop-MRI (Edgedetection)';
     varargout{2}={'SPM8','SPM12'};
+    varargout{3}=['0.6,0.4']; % suggestion for alpha-parameter.
     return
 end
 
 
 Dopt=12;
 maxiter=200;
 
+    disp('Loading images...');
 
 %reslice_nii([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],[options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],[0.5 0.5 0.5]);
 
-reslice_nii([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],[options.root,options.patientname,filesep,'small_',options.prefs.prenii_unnormalized],[4 4 4]);
-reslice_nii([options.root,options.patientname,filesep,options.prefs.rawctnii_unnormalized],[options.root,options.patientname,filesep,'small_',options.prefs.rawctnii_unnormalized],[4 4 4]);
+% MR
+if isfield(options,'usediffmr_coregct')
+    reslice_nii([options.root,options.patientname,filesep,options.usediffmr_coregct],[options.root,options.patientname,filesep,'small_',options.usediffmr_coregct],[2 2 2],0);
+    MR=load_nii_proxi([options.root,options.patientname,filesep,'small_',options.usediffmr_coregct]);
+    delete([options.root,options.patientname,filesep,'small_',options.usediffmr_coregct]);
+
+else
+    reslice_nii([options.root,options.patientname,filesep,options.prefs.prenii_unnormalized],[options.root,options.patientname,filesep,'small_',options.prefs.prenii_unnormalized],[2 2 2],0);
+    MR=load_nii_proxi([options.root,options.patientname,filesep,'small_',options.prefs.prenii_unnormalized]);
+    delete([options.root,options.patientname,filesep,'small_',options.prefs.prenii_unnormalized]);
+
+end
 
+% CT
+reslice_nii([options.root,options.patientname,filesep,options.prefs.rawctnii_unnormalized],[options.root,options.patientname,filesep,'small_',options.prefs.rawctnii_unnormalized],[2 2 2],0);
+CT=load_nii_proxi([options.root,options.patientname,filesep,'small_',options.prefs.rawctnii_unnormalized]);
+
+delete([options.root,options.patientname,filesep,'small_',options.prefs.rawctnii_unnormalized]);
+
+    disp('Done. Smoothing...');
+    MR.img(MR.img<100)=0; % remove noise around brain.
+    MR.img=smooth3(MR.img,'gaussian',[11 11 11]);
+    CT.img(CT.img<0)=0; % remove negative hounsfield parts.
+    CT.img=smooth3(CT.img,'gaussian',[11 11 11]);
+
 
 vizz=1; % visualization on
 alphas=options.coregct.coregthreshs;
 %% estimate
-disp('Loading images...');
-CT=load_nii_proxi([options.root,options.patientname,filesep,'small_',options.prefs.rawctnii_unnormalized]);
-MR=load_nii_proxi([options.root,options.patientname,filesep,'small_',options.prefs.prenii_unnormalized]);
-delete([options.root,options.patientname,filesep,'small_',options.prefs.rawctnii_unnormalized]);
-delete([options.root,options.patientname,filesep,'small_',options.prefs.prenii_unnormalized]);
 
-disp('Done. Smoothing...');
-MR.img(MR.img<100)=0; % remove noise around brain.
-MR.img=smooth3(MR.img,'gaussian',[11 11 11]);
-CT.img(CT.img<0)=0; % remove negative hounsfield parts.
-CT.img=smooth3(CT.img,'gaussian',[11 11 11]);
+
+
 
 if vizz
-    h=figure('color','w','name','Coregistering CT to MR...','NumberTitle','off');
+    ctmr=figure('color','w','name','Coregistering CT to MR...','NumberTitle','off','Toolbar','none','MenuBar','none','DockControls','off','WindowButtonMotionFcn',@ea_mouseMove);
     axis equal
     axis off
 end
@@ -101,10 +117,13 @@
         if D<priorD % improvement
             fprintf('\n %.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f \n\n',[D;M(:)]');
             if vizz
-                plot3(ptMR(1,:),ptMR(2,:),ptMR(3,:),'.','Color',[0.8,0.2,0.8]);
+                set(0,'CurrentFigure',ctmr); 
+                plot3(ptMR(1,:),ptMR(2,:),ptMR(3,:),'.','Color',[0,188/255,226/255]);
                 hold on
-                plot3(ptrCT(1,:),ptrCT(2,:),ptrCT(3,:),'.','Color',[0.2,0.8,0.8]);
+                plot3(ptrCT(1,:),ptrCT(2,:),ptrCT(3,:),'.','Color',[247/255,133/255,20/255]);
                 hold off
+                axis off
+                axis equal
                 drawnow
             end
 
@@ -147,7 +166,11 @@
 matlabbatch{1}.spm.util.reorient.transform.transM = M;
 matlabbatch{1}.spm.util.reorient.prefix = 'r';
 jobs{1}=matlabbatch;
+try
 cfg_util('run',jobs);
+catch
+    warning('Pre-coregistration did not work. Please choose a different threshold.');
+end
 clear jobs matlabbatch
 
 
@@ -179,8 +202,15 @@
 cfg_util('run',jobs);
 clear matlabbatch jobs;
 
+% keep users naming scheme:
+try
+movefile([options.root,options.patientname,filesep,'r',options.prefs.rawctnii_unnormalized],[options.root,options.patientname,filesep,options.prefs.ctnii_coregistered]);
+end
 
 
+function ea_mouseMove(object, eventdata)
+[az,el]=view;
+view(az+1,el);
 
 
 function S=ea_mapvol(X,S,mat) % X= input image (moving), S=space of fixed image (and output), mat=transformation matrix
@@ -197,25 +227,6 @@
 
 
 
-function Y=ea_detect_edges_3d(X,alpha)
-
-%% function detect_edges_3d for Nii-Images
-% Andreas Horn, 2014
-% in: X (volume Matrix)
-% alfa: threshold. Default is 0.1
-
-
-Y=X;
-dimensionality=size(X,3);
-ea_dispercent(0,'Sampling');
-
-for slice=1:dimensionality
-    edgedslice=ea_edgedetection(squeeze(X(:,:,slice)),alpha);
-    Y(1:end-1,1:end-1,slice)=edgedslice;
-    ea_dispercent(slice/dimensionality);
-end
-ea_dispercent(100,'end');
-
 
 
 

diff --git a/ea_coregctmri_edgedetect_and_segment.m b/ea_coregctmri_edgedetect_and_segment.m
@@ -0,0 +1,21 @@
+function varargout=ea_coregctmri_edgedetect_and_segment(options)
+% __________________________________________________________________________________
+% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
+% Andreas Horn
+
+if ischar(options) % return name of method.
+    varargout{1}='Coregister postop-CT with preop-MRI (Edgedetection+Segment)';
+    varargout{2}={'SPM8','SPM12'};
+    varargout{3}=['0.6,0.4']; % suggestion for alpha-parameter.
+    return
+end
+
+if ~exist([options.root,options.patientname,filesep,'c',options.prefs.prenii_unnormalized],'file')
+    ea_nc_segment(options);
+end
+
+%% run standard coregistration
+
+options.usediffmr_coregct=['c',options.prefs.prenii_unnormalized];
+
+ea_coregctmri_edgedetect(options);
diff --git a/ea_coregctmri_edgedetect_and_segment_imtbx.m b/ea_coregctmri_edgedetect_and_segment_imtbx.m
@@ -0,0 +1,28 @@
+function varargout=ea_coregctmri_edgedetect_and_segment_imtbx(options)
+% __________________________________________________________________________________
+% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
+% Andreas Horn
+
+if ischar(options) % return name of method.
+    varargout{1}='Coregister postop-CT with preop-MRI (Edgedetection+Segment, use ML imagetoolbox)';
+    if exist('edge.m','file') % check for imtbx.
+    varargout{2}={'SPM8','SPM12'};
+    else
+        varargout{2}={};
+    end
+    varargout{3}=['0.9']; % suggestion for alpha-parameter.
+    return
+end
+
+if ~exist([options.root,options.patientname,filesep,'c',options.prefs.prenii_unnormalized],'file')
+
+    ea_nc_segment(options);
+end
+
+
+
+%% run standard coregistration
+
+options.usediffmr_coregct=['c',options.prefs.prenii_unnormalized];
+
+ea_coregctmri_edgedetect_imtbx(options);