Changed: Added some flags to waitbar window in cat_progressbar to pre…

…vent

         unwished popping up of the window.
Added:   New function to calculate laterality index for VBM data.

Changed paths:
MM CHANGES.txt
MM cat_batch_bids.sh
MM cat_batch_cat.sh
MM cat_batch_long.sh
 M cat_progress_bar.m
A  cat_vol_laterality_index.m

CHANGES.txt

@@ -1,4 +1,18 @@
 ------------------------------------------------------------------------
+r2476 | gaser | 2023-11-10 16:02:32
+
+Changed paths:
+MM CHANGES.txt
+MM cat_batch_bids.sh
+MM cat_batch_cat.sh
+MM cat_batch_long.sh
+ M cat_progress_bar.m
+A  cat_vol_laterality_index.m
+
+Changed: Added some flags to waitbar window in cat_progressbar to prevent 
+         unwished popping up of the window.
+Added:   New function to calculate laterality index for VBM data.
+------------------------------------------------------------------------
 r2475 | gaser | 2023-11-10 12:08:18
 
 Changed paths:
@@ -39,7 +53,7 @@ Changed paths:
 
 Changed: Set default surface processing back to 22 (CS2).
 Added:   New function to calculate laterality index for volumes.
-Fixed:   Corrected error in cat_batch_bids.sh wehre cat12 folder was not correctly
+Fixed:   Corrected error in cat_batch_bids.sh where cat12 folder was not correctly
          defined.
 ------------------------------------------------------------------------
 r2470 | gaser | 2023-11-08 21:43:04

cat_progress_bar.m

@@ -39,6 +39,9 @@ function cat_progress_bar(action,varargin)
         catch
           Fwaitbar = waitbar(0,arg2);
         end
+
+        % don't know whether this works, but I have used the parameters from spm_progress_bar
+        set(Fwaitbar,'IntegerHandle','off','InvertHardcopy','on','PaperPositionMode','auto','Tag','Interactive');
 
     % Set
     %-------------------------------------------------------------------

cat_vol_laterality_index.m

@@ -0,0 +1,72 @@
+function cat_vol_laterality_index(P)
+% ______________________________________________________________________
+% Calculation of laterality index for images in MNI152NLin2009cAsym space
+% LI = (L-R)/(R+L)
+%
+% 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
+% the values in the opposite hemisphere would be simply inverted and other-
+% wise identical except for the sign.
+%
+% ______________________________________________________________________
+%
+% Christian Gaser, Robert Dahnke
+% Structural Brain Mapping Group (https://neuro-jena.github.io)
+% Departments of Neurology and Psychiatry
+% Jena University Hospital
+% ______________________________________________________________________
+% $Id$
+
+fprintf('Warning: This only works with spatially registered images in MNI152NLin2009cAsym space (CAT12.8 or newer)\n');
+
+if ~nargin
+  P = spm_select(Inf,'image','Select images for LI estimation',{},pwd,'^T*');
+end
+
+V = spm_vol(P);
+n = size(P,1);
+
+sym_template = '/Users/gaser/Dropbox/GitHub/cat12-templates-atlases/templates_external/y_MNI152NLin2009cAsym_to_MNI152NLin2009cSym.nii';
+Vsym = spm_vol(sym_template);
+wvol = cat_vol_defs(struct('field1',{{sym_template}},'images',{{P}},'interp',5,'modulate',0));
+
+for i = 1:n
+  vol = wvol{1}{i};
+
+  % estimate new dimensions for left/right hemisphere
+  xdim  = size(vol,1);
+  left_xdim = floor(xdim/2);
+
+  % consider off x-dimensions
+  if rem(xdim,2)
+    right_xdim = ceil(xdim/2) + 1;
+  else
+    right_xdim = ceil(xdim/2);
+  end
+
+  % flip values
+  left_data = vol(1:left_xdim,:,:);
+  right_data  = flipud(vol(right_xdim:xdim,:,:)); % image should be flipped
+
+  % estimate laterality index
+	LI = (left_data-right_data)./(left_data+right_data+eps);
+
+  % rename dataname
+  [pth,nm,xt] = spm_fileparts(deblank(P(i,:)));
+  flipped_name = fullfile(pth, ['LI_' nm xt]);
+
+  % we need origin and voxel size from template
+  Vout = Vsym;
+  Vout.fname = flipped_name;
+  Vout.dim = size(LI);
+  Vout.dt(1) = 16;
+  Vout.pinfo(1) = 1;
+  Vout.mat(1,:) = -Vout.mat(1,:);
+  Vout.mat(1,4) = Vout.mat(1,4) - 1.5;
+
+  Vout.descrip = 'Laterality index';
+
+  spm_write_vol(Vout,left_data);
+  fprintf('Save LI in %s\n',flipped_name);
+end