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Hello Jorge,

You can download a tar archive of the pre-built 3rd party packages with the following command,

curl -O http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/centos7-packages.tar.gz

- and the versions of the contained packages in that archive should work: vtk=5.10.1, petsc=2.3.3; itk=4.13.0; gts=0.7.6; ann=1.1.2

You could set the individual cmake variables for each package, or instead try setting -DFS_PACKAGES_DIR to point to the absolute path of where the ./packages subdir is after expanding the archive; then you should not have to individually set ITK_DIR, VTK_DIR, etc.

You could also try downloading “makefile.wiki” from,
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view
to do this and other work for you.

Then if you type “make -f makefile.wiki pkg_download” it will try to download that package archive for you, and also add a python3 (needed for freesurfer) from anaconda python under the packages archive.  If it finds everything, it will generate the cmake command for you.  You can see what the command will be with  "make -f makefile.wiki config_print”.  You can also use it to try and run cmake, then do the build and install passes - type “make -f makefile.wiki help” to read more.

- R.


On May 26, 2019, at 04:25, Jorge Naranjo <jorge.naranjo@nyu.edu> wrote:

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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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