Hi All,

IM compiling freesurfer, after many bumps reached a point i havent figured out how to proceed.

My setup:

Centos7

GCC 4.8.5

Freesurfer 6.0.0

Dependencies as in /usr/pubsw/packages/

- KWWWidgets : CVS-vtk560

- petsc : 2.3.3-p13

- mni 1.5

- tcltktixblt : 8.4.6

- wxWidgets wxGTK-2.8.9

- xawplus: 3.1.0

Dependencies I built and installed in /usr/pubsw/packages/

- dcmtk: 3.6.4

- itk: 4.9.1

- vxl: v1.17.0

The rest of dependencies installed through RPM packages (yum) system-wise.. including VTK, etc ...

then I do:

FS_PACKAGES_DIR=/usr/pubsw/packages
VTK_DIR=/usr
VTK_LIBRARIES=/usr/lib64
PREFIX=/share/apps/NYUAD3/freesurfer/6.0.0
CMAKE_BUILD_TYPE=Release
PETSC_DIR=/usr/pubsw/packages/petsc/current
ITK_DIR=/usr/pubsw/packages/itk/4.9.1/lib/cmake/ITK-4.9/
OpenGL_GL_PREFERENCE=GLVND
DANN_LIBRARIES=/usr/lib64

export CPATH=$CPATH:/usr/pubsw/packages/itk/4.9.1/include/ITK-4.9/

cmake3 ../freesurfer -DFS_PACKAGES_DIR=${FS_PACKAGES_DIR} -DVTK_LIBRARIES=${VTK_LIBRARIES} -DVTK_DIR=${VTK_DIR} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DPETSC_DIR=${PETSC_DIR} -DITK_DIR=${ITK_DIR} -DOpenGL_GL_PREFERENCE=${OpenGL_GL_PREFERENCE} -DANN_LIBRARIES=${DANN_LIBRARIES} -DUSE_PYTHON_INCLUDE_DIR=ON -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib64/ -lglut"

make

NOTE: the glut thing is because if I let the system use the libglut inside packages dir in the source code ... compilation breaks with :

/bin/ld: ../packages/glut/libglut.a(glut_win.c.o): undefined reference to symbol 'glXCreateContextWithConfigSGIX'

Well, the thing is that will all the above, the compilation breaks with this message:

[ 57%] Built target trk_tools
[ 57%] Built target streamlineFilter
[ 57%] Built target testOrientationPlanesFromParcellation
[ 57%] Building CXX object anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o
/scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx: In function ‘int main(int, char**)’:
/scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx:648:62: error: expected primary-expression before ‘double’
vcl_vector<unsigned int> assign = vnl_hungarian_algorithm<double>( distances ); //.GetAssignmentVector();
^
make[2]: *** [anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o] Error 1
make[1]: *** [anatomicuts/CMakeFiles/dmri_match.dir/all] Error 2
make: *** [all] Error 2

Any help !?? will be highly appreciated

thanks!

Jorge A. Naranjo
HPC Computational Specialist
NYU Abu Dhabi

Office Tel (UAE): +971 2 628 4750
Mobile (UAE): +971 56 319 2814

New York University - Abu Dhabi (NYUAD)

Saadiyat Campus - A2, Room-131

P.O. Box 129188
Abu Dhabi, United Arab Emirates

http://nyuad.nyu.edu
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