Merge pull request #375 from rcwelsh/ConnTool_alpha_rcw

hotfix for ConnTool

Author: dankessler

ConnTool/Code/SOM_WriteNII.m

@@ -44,7 +44,16 @@
   return
 end
 
-if any(volDIM(1:3)-size(niftiIn.dat(:,:,:,1)))
+niiDIM = size(niftiIn.dat(:,:,:,1));
+
+% Needed to add this in case the "template" image was also two-dimensional
+% Robert Welsh - 2015-10-29
+
+if length(niiDIM) < length(volDIM)
+    niiDIM = [niiDIM 1];
+end
+
+if any(volDIM(1:3)-niiDIM)
   SOM_LOG(sprintf('FATAL ERROR : TemplateImage dimension doesn''t match data dimension to be written\n'));
   return 
 end

ConnTool/ConnTool_batch_mc_central.m

@@ -193,7 +193,7 @@
                 if (MotionDeriv)
                     RealignmentParametersQuad = [RealignmentParameters RealignmentParametersDerivR].^2;
                 else
-                    RealignmentParametersQuad = RealignmenParameters.^2;
+                    RealignmentParametersQuad = RealignmentParameters.^2;
                 end
 
                 parameters.data.run(iRun).MotionParameters = [RealignmentParameters];