Just wanted to report back a success. I had to do some fixes so hope this helps anybody.

My gpus are GTX1080Ti and the CPU involved is E5-2620 dual 10 core on this server.

The vanilla cpu recon-all finished in 7 hours, the gpu run finished in 4.3 hours.

Q: I seem to not have any errors or indications why mri_glmfit or mri_robust_register cuda binaries did not compile. Any ideas?

-Henk

In configure file (from previous post) comment out the with_cuda="" line
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046236.html
CUDA_DIR=""
with_cuda=""

In utils/mrifilter.c uncomment line defining 'int width, weight, height'
above the test if (width <=1 || height <=1 || depth <=1) on line 3005

then find Makefiles with incorrect gpu arch for the gpu packages
change architecture from sm_?? to sm_61 (multiple times per file)

which nvcc

export PATH=/usr/local/cuda/bin:$PATH
locate libcuda.so
export LD_LIBRARY_PATH=/usr/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH

./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda
 make clean
make -j 4
make install

yields

./bin/mris_flatten_cuda
./bin/mris_sphere_cuda
./bin/mris_fix_topology_cuda
./bin/mri_segstats_cuda
./bin/mri_em_register_cuda
./bin/mri_vol2vol_cuda
./bin/mris_inflate_cuda
./bin/mri_ca_register_cuda