(1) Fixed: Corrected issue in using other Templates and output resolutions

             in the longitudinal pipeline. Use default 1.5 mm in average processing
             that has to fit to the TPM in cat_long_main. Removed the warning
             for different output resolutions in cat_long_multi_run. Corrected
             definitions in cat_main_registration.
(2) Fixed:   Corrected problem with missing text in the cat_report.
(3) Fixed:   Corrected an bug in writing the affine/rigid background image in
             cat_main_write.
(4) Fixed:   Corrected bug in LAS in case of some image with negative background.

Changed paths:
 M CHANGES.txt
 M cat_long_main.m
 M cat_long_multi_run.m
 M cat_main_LAS.m
 M cat_main_registration.m
 M cat_main_reportfig.m

Author: robdahn

CHANGES.txt

@@ -1,4 +1,24 @@
 ------------------------------------------------------------------------
+r2565 | robertdahnke | 2024-03-14 15:38:20
+
+Changed paths:
+ M CHANGES.txt
+ M cat_long_main.m
+ M cat_long_multi_run.m
+ M cat_main_LAS.m
+ M cat_main_registration.m
+ M cat_main_reportfig.m
+
+(1) Fixed:   Corrected issue in using other Templates and output resolutions
+             in the longitudinal pipeline. Use default 1.5 mm in average processing
+             that has to fit to the TPM in cat_long_main. Removed the warning
+             for different output resolutions in cat_long_multi_run. Corrected
+             definitions in cat_main_registration.   
+(2) Fixed:   Corrected problem with missing text in the cat_report. 
+(3) Fixed:   Corrected an bug in writing the affine/rigid background image in 
+             cat_main_write.
+(4) Fixed:   Corrected bug in LAS in case of some image with negative background. 
+------------------------------------------------------------------------
 r2564 | gaser | 2024-03-10 19:24:34
 
 Changed paths:

cat_long_main.m

@@ -529,13 +529,20 @@
       end
     end
   end
-
+  
   % RD202102: differentiation between user levels not tested yet !
   if exist('extopts','var') && isfield(extopts,'bb')
     matlabbatch{mbi}.spm.tools.cat.estwrite.extopts.bb              = 1; % use TPM output BB 
   elseif exist('extopts','var') &&  isfield(extopts,'registration') && isfield(extopts.registration,'bb')
     matlabbatch{mbi}.spm.tools.cat.estwrite.extopts.registration.bb = 1; % use TPM output BB 
   end
+  % RD202403: run average for 1.5 mm to combine it with the TPM 
+  if exist('extopts','var') && isfield(extopts,'vox')
+    matlabbatch{mbi}.spm.tools.cat.estwrite.extopts.vox = 1.5; 
+  elseif exist('extopts','var') &&  isfield(extopts,'registration') && isfield(extopts.registration,'vox')
+    matlabbatch{mbi}.spm.tools.cat.estwrite.extopts.registration.vox = 1.5; 
+  end
+
 
   if exist('output','var') && ~isempty(output)
     matlabbatch{mbi}.spm.tools.cat.estwrite.output            = output;

cat_long_multi_run.m

@@ -14,13 +14,6 @@
 
 if isdeployed, job.nproc = 0; end
 
-if isfield(job.extopts,'vox') && job.extopts.vox ~= 1.5
-  job.extopts.vox = 1.5;
-  fprintf('\n---------------------------------------------------------------------------\n');
-  fprintf('Warning: No change of output voxel size possible for longitudinal pipeline!\n');
-  fprintf('---------------------------------------------------------------------------\n');
-end
-
 % use some options from GUI or default file
 opts        = job.opts;
 extopts     = job.extopts;

cat_main_LAS.m

@@ -802,7 +802,9 @@
   end
  else
    % simple 
-   Ynb   = smooth3( Ycls{6})>128 & Yg<0.3; 
+   % RD202403: avoid skull-stripped voxels and neighbors
+   Ynb   = smooth3( Ycls{6})>128 & Yg<0.3 & ...
+     ~cat_vol_morph(Yg==0,'d'); % avoid arificial regions
    %Ynb   = cat_vol_morph(Ynb,'e',4*vxv); 
 
    Ylab{3} = ones(size(Ygm),'single') .* min( [ T3th(1)                   , cat_stat_nanmean(Ysrc(Ycm(:))) ] ); 
@@ -813,12 +815,13 @@
   Ylab{1} = Ylab{1} .* T3th(2) / cat_stat_kmeans( Ylab{1}(Ygm(:)>0.5), 1); 
   Ylab{3} = Ylab{3} .* T3th(1) / cat_stat_kmeans( Ylab{3}(Ycm(:)>0.5), 1); 
 
-  % RD202110: corrected cases with incorrect background region Ynb
+  %% RD202110: corrected cases with incorrect background region Ynb
+  %  RD202403: there are allways some voxels .. somegthing is wrong here 
+  %if sum(Ynb(:)>0.5)>0
+  %  Ynb   = smooth3( Ycls{6})>128 & Yg<0.3; 
+  %end
   if sum(Ynb(:)>0.5)>0
-    Ynb   = smooth3( Ycls{6})>128 & Yg<0.3; 
-  end
-  if sum(Ynb(:)>0.5)>0
-    Ylab{6} = Ylab{6} .* cat_stat_kmeans( Ysrc(Ynb(:)>0.5) , 1) / max(eps,cat_stat_kmeans( Ylab{6}(Ynb(:)>0.5) , 1)); 
+    Ylab{6} = Ylab{6} .* abs(cat_stat_kmeans( Ysrc(Ynb(:)>0.5) , 1)) / max(eps,abs(cat_stat_kmeans( Ylab{6}(Ynb(:)>0.5) , 1))); 
   else
     Ylab{6} = min(Ysrc(:)); 
   end

cat_main_registration.m

@@ -340,12 +340,14 @@
       % M0 for the individual volume
       % M1* for the different normalized spaces
       % Mad for the Dartel template with different BB as the TPM
-      M0   = res.image.mat;          
-      if isfield( job.extopts , 'bb' )  &&  numel( job.extopts.bb ) == 1  && job.extopts.bb == 1
-        M1 = tpmM;
-      else
-        imat = spm_imatrix(tmpM); imat(1:3) = imat(1:3) + imat(7:9).*(tdim - (newres/tmpres*odim))/2; imat(7:9) = imat(7:9) * newres/tmpres; M1   = spm_matrix(imat);
-      end
+      M0   = res.image.mat; 
+      % RD202403: modified to support output of the given voxel size vox - see also below. cleanup later. 
+      %if isfield( job.extopts , 'bb' )  &&  numel( job.extopts.bb ) == 1  && job.extopts.bb == 1 %&& job.extopts.vox == abs(tmpM(1))
+      %  M1   = tpmM;  
+      %  imat = spm_imatrix(tmpM); imat(1:3) = imat(1:3) + imat(7:9).*(tdim - (newres/tmpres*odim))/2; imat(7:9) = imat(7:9) * newres/tmpres; M1   = spm_matrix(imat);
+      %else
+      imat = spm_imatrix(tmpM); imat(1:3) = imat(1:3) + imat(7:9).*(tdim - (newres/tmpres*odim))/2; imat(7:9) = imat(7:9) * newres/tmpres; M1   = spm_matrix(imat);
+      %end
       imat = spm_imatrix(eye(4)); imat(1:3) = imat(1:3) + imat(7:9).*(tdim - (newres/tmpres*odim))/2; imat(7:9) = imat(7:9) * newres/tmpres; Mad  = spm_matrix(imat);
 
       % affine and rigid parameters for registration 
@@ -468,12 +470,12 @@
         % mat matrices for different spaces
         % - here M1 == M1t
         M0     = res.image.mat;                                                       % for (interpolated) individual volume
-        if isfield( job.extopts , 'bb' )  &&  numel( job.extopts.bb ) == 1  && job.extopts.bb == 1
-          M1   = tpmM;
-        else
-          imat = spm_imatrix(tmpM); imat(1:3) = imat(1:3) + imat(7:9).*(tdim - (newres/tmpres*odim))/2; imat(7:9) = imat(7:9) * newres/tmpres; 
-          M1   = spm_matrix(imat);
-        end
+        % RD202403: modified to support output of the given voxel size vox - see also above. cleanup later.
+        %if isfield( job.extopts , 'bb' )  &&  numel( job.extopts.bb ) == 1  && job.extopts.bb == 1
+        %  M1   = tpmM;
+        %else
+        imat = spm_imatrix(tmpM); imat(1:3) = imat(1:3) + imat(7:9).*(tdim - (newres/tmpres*odim))/2; imat(7:9) = imat(7:9) * newres/tmpres; M1   = spm_matrix(imat);
+        %end
 
         % estimate the inverse transformation 
         yid             = spm_diffeo('invdef', Yy , sdim, inv(tpmM\M1), M1\res.Affine*M0); 

cat_main_reportfig.m

@@ -42,6 +42,23 @@ function cat_main_reportfig(Ym,Yp0,Yl1,Psurf,job,qa,res,str)
   fg  = spm_figure('FindWin','Graphics'); 
   set(0,'CurrentFigure',fg)
 
+  % remove CAT12 figure background image from start
+  try
+    fgc = get(fg,'Children');
+    if ~isempty(fgc)
+      fgcc = get(fgc,'Children');
+      if ~isempty(fgcc)
+        % remove figure elements to prevent further interations
+        delete(fgcc);
+        spm_figure('Clear',fg)
+        
+        % run the reportfig function the first time to fully clear the 
+        % changes by the cat start figure
+        cat_main_reportfig(Ym,Yp0,Yl1,[],job,qa,res,str)
+      end
+    end
+  end
+
   def.extopts.report.useoverlay   = 2;  % different p0 overlays, described below in the Yp0 print settings
                                         % (0 - no, 1 - red mask, 2 - blue BG, red BVs, WMHs [default] ... )
   def.extopts.report.type         = 2;  % (1 - Yo,Ym,Yp0,CS-top, 2 - Yo,Yp0,CS-left-right-top)