Added: Added new deformation field for getting symmetrical spatially …

…registered

         images for estimating laterality index.
Changed: Updated path of symmetrical deformation field.

Changed paths:
 M CHANGES.txt
 M cat_run_job1639.m
 M cat_vol_laterality_index.m
A  templates_MNI152NLin2009cAsym/y_MNI152NLin2009cAsym_to_MNI152NLin2009cSym.nii

CHANGES.txt

@@ -1,4 +1,16 @@
 ------------------------------------------------------------------------
+r2478 | gaser | 2023-11-13 15:41:36
+
+Changed paths:
+ M CHANGES.txt
+ M cat_run_job1639.m
+ M cat_vol_laterality_index.m
+A  templates_MNI152NLin2009cAsym/y_MNI152NLin2009cAsym_to_MNI152NLin2009cSym.nii
+
+Added:   Added new deformation field for getting symmetrical spatially registered 
+         images for estimating laterality index.
+Changed: Updated path of symmetrical deformation field.
+------------------------------------------------------------------------
 r2477 | gaser | 2023-11-13 11:35:53
 
 Changed paths:

cat_run_job1639.m

@@ -828,6 +828,7 @@ function cat_run_job1639(job,tpm,subj)
             if (length(ff)>4 && strcmp(ff(1:5),'navg_')) || ...
                (isfield(job,'useprior') && ~isempty(job.useprior)) || ...
                (isfield(job.extopts,'new_release') && job.extopts.new_release)
+              fprintf('\n');
               cat_io_cprintf('g8','  Use new longitudinal background setting. ');
               % new minimal masking approach in longitudinal processing to avoid backgound peak erros and for future releases 
               Ymsk        = cat_vol_morph( ~Ybg ,'dd',10,vx_vol) & ...          % remove voxels far from head

cat_vol_laterality_index.m

@@ -3,6 +3,9 @@ function cat_vol_laterality_index(P)
 % Calculation of laterality index for images in MNI152NLin2009cAsym space
 % LI = (L-R)/(R+L)
 %
+% We apply the deformation from MNI152NLin2009cAsym to the symmetrical template
+% MNI152NLin2009cSym in order to obtain a symmetrical image, which then can be
+% used to estimate laterality index.
 % The result is indicated with a prepended 'LI_' in the dataname
 % of the file.
 % Please note that only the data of the left hemipshere is stored, since
@@ -24,41 +27,42 @@ function cat_vol_laterality_index(P)
   P = spm_select(Inf,'image','Select images for LI estimation',{},pwd,'^w.*');
 end
 
-sym_template = '/Users/gaser/Dropbox/GitHub/cat12-templates-atlases/templates_external/y_MNI152NLin2009cAsym_to_MNI152NLin2009cSym.nii';
-Vsym = spm_vol(sym_template);
+Def_sym = fullfile(cat_get_defaults('extopts.pth_templates'),'y_MNI152NLin2009cAsym_to_MNI152NLin2009cSym.nii');
+Vsym = spm_vol(Def_sym);
 
 n = size(P,1);
 
 cat_progress_bar('Init',n);
 
 for i = 1:n
   name = deblank(P(i,:));
-  V = spm_vol(name);
-  wvol = cat_vol_defs(struct('field1',{{sym_template}},'images',{{name}},'interp',5,'modulate',0));
+
+  % apply deformation to selected images
+  wvol = cat_vol_defs(struct('field1',{{Def_sym}},'images',{{name}},'interp',5,'modulate',0));
 
   vol = wvol{1}{1};
 
   % estimate new dimensions for left/right hemisphere
   xdim  = size(vol,1);
-  left_xdim = floor(xdim/2);
+  right_xdim = floor(xdim/2);
 
-  % consider off x-dimensions
+  % consider odd x-dimensions
   if rem(xdim,2)
-    right_xdim = ceil(xdim/2) + 1;
+    left_xdim = ceil(xdim/2) + 1;
   else
-    right_xdim = ceil(xdim/2);
+    left_xdim = ceil(xdim/2);
   end
 
   % flip values
-  left_data = vol(1:left_xdim,:,:);
-  right_data  = flipud(vol(right_xdim:xdim,:,:)); % image should be flipped
+  left_data  = flipud(vol(left_xdim:xdim,:,:)); % image should be flipped
+  right_data = vol(1:right_xdim,:,:);
   mx = max(vol(:));
 
   % estimate laterality index
-	LI = (right_data-left_data)./(left_data+right_data+eps);
+	LI = (left_data-right_data)./(left_data+right_data+eps);
 
-	% and exclude areas where intensity of tissue is quite low
-	LI((left_data+right_data)<0.01*mx) = 0;
+	% and exclude areas where intensity (i.e. of tissue) is quite low
+	LI(abs(left_data+right_data)<0.01*mx) = 0;
 
   % rename dataname
   [pth,nm,xt] = spm_fileparts(deblank(P(i,:)));
@@ -70,13 +74,15 @@ function cat_vol_laterality_index(P)
   Vout.dim = size(LI);
   Vout.dt(1) = 16;
   Vout.pinfo(1) = 1;
+
+  % flipping is necessary
   Vout.mat(1,:) = -Vout.mat(1,:);
 
-  Vout.descrip = 'Laterality index';
+  Vout.descrip = 'Laterality index (L-R)/(R+L)';
 
   spm_write_vol(Vout,LI);
   fprintf('Save LI in %s\n',flipped_name);
-cat_progress_bar('Set',i);
+  cat_progress_bar('Set',i);
 end
 
 cat_progress_bar('Clear');