Index: /issm/trunk-jpl/patches/issm_options.m4
===================================================================
--- /issm/trunk-jpl/patches/issm_options.m4	(revision 15116)
+++ /issm/trunk-jpl/patches/issm_options.m4	(revision 15117)
@@ -115,6 +115,6 @@
 
 		AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT)
-  		MATLABINCL=-I `cygpath -wa /cygdrive/c/Program\ Files/MATLAB/R2011b/extern/include`;
-		
+  		MATLABINCL="-I$MATLAB_ROOT/extern/include"
+
 		dnl 4. get MEXLIB MEXLINK and MEXEXT (experimental)
       dnl OS-dependent variables and checks
@@ -148,7 +148,9 @@
   			*cygwin*) 
   				if  test $VENDOR = intel-win7-32; then
-  					MEXLIB="/link /DLL /export:mexFunction libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib libf2cblas.lib libf2clapack.lib" 
+					MATLABLIB="$MATLAB_ROOT/extern/lib/win32/microsoft"
+  					MEXLIB="/link /DLL /export:mexFunction libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib" 
   				elif  test $VENDOR = intel-win7-64; then
-  					MEXLIB="/DLL /export:mexFunction -L$MATLAB_ROOT\extern\lib\win64\microsoft\ libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib  -NOLOGO -INCREMENTAL:NO -manifest" 
+					MATLABLIB="$MATLAB_ROOT/extern/lib/win64/microsoft"
+  					MEXLIB="/link /DLL /export:mexFunction -L$MATLABLIB libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib " 
   				fi
   				MEXEXT=`$MATLAB_ROOT/bin/mexext.bat`