Corrected: Display og white background in slice_overlay was not correct.

Changed paths:
 M CHANGES.txt
 M Contents.m
 M Makefile
 M cat_plot_boxplot.m
 M doc/cat.html
 M doc/index.html
 M slice_overlay.m

CHANGES.txt

@@ -1,3 +1,17 @@
+------------------------------------------------------------------------
+r2621 | gaser | 2024-12-07 23:02:18
+
+Changed paths:
+ M CHANGES.txt
+ M Contents.m
+ M Makefile
+ M cat_plot_boxplot.m
+ M doc/cat.html
+ M doc/index.html
+ M slice_overlay.m
+
+Corrected: Display og white background in slice_overlay was not correct.
+
 ------------------------------------------------------------------------
 r | dahnke | 2024-09-27 18:26:57
 

Contents.m

@@ -1,5 +1,5 @@
 % Computational Anatomy Toolbox
-% Version 2583 (CAT12.9) 2024-05-25
+% Version 2620 (CAT12.9) 2024-10-11
 % ______________________________________________________________________
 %
 % Christian Gaser, Robert Dahnke

Makefile

@@ -211,7 +211,7 @@ precompile:
 	-@echo    cd spm12/config
 	-@echo    spm_make_standalone
 #	-@echo    "Ubuntu 19.10 (run spm12_R2017b on paris to compile) : mv /Users/gaser/spm/standalone/spm12.ctf ${PRECOMPILED}/MCR_Linux/"
-	-@echo    "Ubuntu 17.10 (run spm12_R2017b with desktop on MacBook to compile) : mv /Users/gaser/spm/standalone/spm12.ctf ${PRECOMPILED}/MCR_Linux/"
+	-@echo    "Ubuntu 17.10/19.10 (run spm12_R2017b with desktop on MacBook to compile) : mv /Users/gaser/spm/standalone/spm12.ctf ${PRECOMPILED}/MCR_Linux/"
 	-@echo    "Windows 10: mv /Users/gaser/spm/standalone/spm12.[ce][tx][fe] ${PRECOMPILED}/MCR_Win/"
 	-@echo    "MacOS (run spm12_R2023b_intel): rm -rf ${PRECOMPILED}/MCR_Mac/spm12.app; mv /Users/gaser/spm/standalone/spm12.app ${PRECOMPILED}/MCR_Mac/"
 	-@echo    "MacOS ARM64 (run spm12_R2023b): rm -rf ${PRECOMPILED}/MCR_Mac_arm64/spm12.app; mv /Users/gaser/spm/standalone/spm12.app ${PRECOMPILED}/MCR_Mac_arm64/"

cat_plot_boxplot.m

@@ -89,7 +89,7 @@
 % opt.notched = ['x','*'] points between 1.5 and 3 times the IQR is marked with
 % 'x' and points outside 3 times IQR with '*'.
 % opt.vertical = 0 makes the boxes horizontal, by default opt.vertical = 1.
-% maxwhisker defines the length of the wh^1iskers as a function of the IQR
+% maxwhisker defines the length of the whiskers as a function of the IQR
 % (default = 1.5). If maxwhisker = 0 then boxplot displays all data  
 % values outside the box using the plotting opt.notched for points that lie
 % outside 3 times the IQR.   

doc/cat.html

@@ -9,7 +9,7 @@
 
     <div id="content">
       <br />
-      <p align="center" style="text-align:center;">This is <b>CAT12.9 (r2583) from 2024-05-25</b><br />You can update your copy of CAT12 here: <a href="matlab:cat_update(1);">Check for update</a>.<br />If you find any bug, please report them at <a href="mailto:vbmweb@gmail.com">vbmweb@gmail.com</a>.</p>
+      <p align="center" style="text-align:center;">This is <b>CAT12.9 (r2620) from 2024-10-11</b><br />You can update your copy of CAT12 here: <a href="matlab:cat_update(1);">Check for update</a>.<br />If you find any bug, please report them at <a href="mailto:vbmweb@gmail.com">vbmweb@gmail.com</a>.</p>
       <h1 style="text-align:center;"><img src="images/CAT.png" width=40% height=auto alt="CAT" ></h1>
 
       <hr />
@@ -33,7 +33,7 @@ <h2>Description</h2>
       Please <a href="matlab:web(fullfile(fileparts(which('cat12')),'doc','index.html#cite'),'-new');">cite our papers</a> and the work of other researchers if you use this software.</p><p>
       Our main paper is:<br>
       Gaser C, Dahnke R, P.M. Thompson, Kurth K, Luders E, Alzheimer's Disease Neuroimaging Initiative.<br>
-      <a href="matlab:web('https://www.biorxiv.org/content/10.1101/2022.06.11.495736','-new');">A Computational Anatomy Toolbox for the Analysis of Structural MRI Data.</a>
+      <a href="matlab:web('https://doi.org/10.1093/gigascience/giae049','-new');">CAT: a computational anatomy toolbox for the analysis of structural MRI data.</a>
       </p>
     </div>        
 

doc/index.html

@@ -3741,7 +3741,7 @@ <h2 id="faq">FAQ</h2>
 
             <details>            
               <summary><u>Which of the morphological measures (grey matter or cortical thickness) is the best to assess atrophy/neurodegeneration in Alzheimer's disease?</u></summary>
-              Cortical thickness is the better biological measure of Alzheimer's disease, while grey matter volume is more sensitive. This is because surface reconstruction is more susceptible to image quality problems and thickness is estimated in the sub-millimetre range, whereas images have a spatial resolution of about 1 mm. In Alzheimer's disease, however, atrophy is quite pronounced, so cortical thickness is also a reliable indicator of these effects. Grey matter volume, on the other hand, has the advantage of providing additional measurements in the hippocampus and amygdala, which are key structures in Alzheimer's disease. I would definitely try both and decide based on the results.
+              Cortical thickness is the better biological measure of Alzheimer's disease, while grey matter volume is more sensitive. This is because surface reconstruction is more susceptible to image quality problems and thickness is estimated in the sub-millimeter range, whereas images have a spatial resolution of about 1 mm. In Alzheimer's disease, however, atrophy is quite pronounced, so cortical thickness is also a reliable indicator of these effects. Grey matter volume, on the other hand, has the advantage of providing additional measurements in the hippocampus and amygdala, which are key structures in Alzheimer's disease. I would definitely try both and decide based on the results.
             </details>            
 
             <details>            

slice_overlay.m

@@ -1,4 +1,4 @@
-function varargout = slice_overlay(action, varargin);
+function varargout = slice_overlay(action, varargin)
 % Function to display + manage slice display 
 % Slice display works on a global structure SO
 % with fields 
@@ -410,6 +410,8 @@
     end
     % transpose to reverse X and Y for figure
     i1 = reshape(i1, vdims(1:2))';
+    % make white background if defined
+    if all(SO.bkg_col == [1 1 1]), i1(i1==0) = 1; end
     % rescale to colormap
     [csdata badvals]= scaletocmap(...
       i1,...
@@ -426,12 +428,10 @@
       img(tmp) = iimg(tmp);
     end
   end
+
   % threshold out of range values
   img(img>1) = 1;
-
-  % make white background if defined
-  if all(SO.bkg_col == [1 1 1]), img(img==0) = 1; end
-
+
   image('Parent', axisd(i),...
     'ButtonDownFcn', SO.callback,...
     'CData',img);