retroactive commit, alpha20

niftimatlib/matlab/spm_flip_analyze_images.m

@@ -0,0 +1,19 @@
+function flip = spm_flip_analyze_images
+% Do Analyze format images need to be left-right flipped? The default
+% behaviour is to have the indices of the voxels stored as left-handed and
+% interpret the mm coordinates within a right-handed coordinate system.
+%
+% Note: the behaviour used to be set in spm_defaults.m, but this has now
+% been changed.
+%__________________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+% John Ashburner
+% Id: spm_flip_analyze_images.m 1418 2008-04-15 19:15:16Z john 
+
+%
+% niftilib $Id: spm_flip_analyze_images.m,v 1.3 2012/03/22 18:36:33 fissell Exp $
+%
+
+flip = 1;
+

palm_backend.m

@@ -664,7 +664,7 @@ function palm_backend(varargin)
             % Compute the combined statistic
             Gnpc = cat(1,G{:,c});
             T{c} = fastnpc(Gnpc,cat(1,df2{:,c}));
-            
+
             % Since computing the parametric p-value for some methods
             % can be quite slow, it's faster to run all these checks
             % to ensure that 'pparanpc' runs just once.

palm_gpval.m

@@ -55,6 +55,7 @@
     if any(in(:)),
         pvals(ic) = palm_gpval(G(in),0);
     end
+    pvals = reshape(pvals,size(G));
 
 elseif df1 == 0,
 

palm_help.m

@@ -139,8 +139,7 @@ function palm_help(varargin)
 fprintf('	removed.\n\n');
 
 fprintf('-twotail : Run two-tailed tests for all the t-contrasts instead of\n');
-fprintf('	one-tailed. If NPC is used, it also becomes two-tailed for the\n');
-fprintf('	methods which statistic are symmetric around zero under the null.\n\n');
+fprintf('	one-tailed. If NPC is used, it naturally becomes two-tailed\n\n');
 
 fprintf('-advanced : Show advanced options.\n\n');