Notes on building VXL for MGH Freesurfer:

Here is how v1.13.0 was installed:

  cd /usr/pubsw/packages/vxl
  mkdir 1.13.0
  ln -s 1.13.0 current
  cd current
  unzip <wherever>/vxl-1.13.0.zip 
  mv vxl-1.13.0 src
  cd src
  ccmake .

<wherever> is the path to the source tarball,
which can be found at:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/src
or at the VXL homepage.

ccmake brings-up the setup utility.  All BUILD_ packages 
should be set to OFF, except for the VNL numerics and 
utilities packages, and tests.  Static libs are built
to spare the grief of dealing with LD_LIBRARY_PATH, but
freesurfer does not prevent building and using shared libs 
in a custom installation, like a laptop or home computer.
The SSE instructions are used so that 32b platform results
match those on the 64b platform (which uses SSE by default).
The install path (CMAKE_INSTALL_PATH) is also updated. 
So these are the things to check in the ccmake screen:

  BUILD_<something>	OFF, except for:

  BUILD_CORE_NUMERICS	  ON
  BUILD_CORE_UTILITIES	ON
  BUILD_SHARED_LIBS	    OFF
  BUILD_TESTING		      ON
  CMAKE_BUILT_TYPE      Release
  CMAKE_INSTALL_PREFIX	/usr/pubsw/packages/vxl/1.13.0
  CMAKE_CXX_FLAGS       -msse2 -mfpmath=sse
  CMAKE_C_FLAGS         -msse2 -mfpmath=sse

Press 'c' a couple times, then 'g' to generate the 
makefile.  Then:

  make
  make test
  make install
  make clean
  cd /usr/pubsw/packages/vxl
  ./fix_perms.csh

All tests run during make test should pass (at least 
they do on the Linux platform).  Some platforms, like
Mac OS X 10.3.9, have problems building the tests, so
those can be set to OFF (ie, re-run ccmake). make install 
creates /lib /include and /share in CMAKE_INSTALL_PREFIX.
make clean deletes the temporary build files.

Running the fix_perms script, which exists only at the
NMR center, ensures that permissions get reset to 
where fsdev groups owns and can write all files.

Nick
1 March 2010