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Hello Christian,

I have not checked 'make check' procedure, 
'recon-all' with my compiled binary was finished without error and 
segmentation results looks nice. It may be OK for my environment.

Using '-use-gpu' and '-openmp 8' flag, the time of 'recon-all' reduced to
around 4 hours from 12 hours without flag in my PC environment
(Xenon E5-2620 [2.00GHz/15M/6Core-12Thread] x 2 + Tesla C2075 6GB x2 ).

At the first time in build freesurfer, I have not known my Tesla GPU
(fermi-architecture of sm_20) was not supported in CUDA 9.1 
(distribution in Ubuntu 18.04 package). I have tried to configure with
'--with-cuda = /usr'.
'make -j4 'was completely finished but cuda related binary 
(such as 'mri_em_register_cuda') have not compiled and not installed.

Then I made '/usr/local/cuda' directory
and include and library path was linked in '/usr/local/cuda' directory
cd /usr/local/cuda
sudo ln -s /usr/include include
sudo ln -s /usr/lib/x86_64-linux-gnu lib
sudo ln -s /usr/bin bin

and NVIDIA_ARCH in 'configure.in' was edited to sm_11 to sm_30,
configure with '--with-cuda=/usr/local/cuda' flag.
It can compiled cuda related binary.

However my GPU architecture does not support sm_30,
'recon-all' was stopped with error of
----------------------------------------------------------------------------------
CUDA Error in file '../include/ctfactory.hpp' on line 96 : invalid texture 
reference.
Abort (core dumped)
---------------------------------------------------------------------------------
After that, I did extract cuda_cluster_pkgs_8.0.61_ubuntu1604.tar.gz and 
compiled
freesufer binary again.

GPU architecture and related CUDA version was reffered in the following URL
http://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/


>P.S. Kazuhiro, I tried your 8-step procedure above, but on step 2 I got an 
>error building vxl that it could not find the '-lgeotiff' flag used in one of 
>the cmake commands. I tried debugging but found no help online. Any advice?

I remeber ubuntu 18.04 package of libgeotiff-dev  was installed 
after vxl compilation error appeared.
You might require
sudo apt install libgeotiff-dev.

--------------------------------------------------------------
Kazuhiro Nakamura, Ph.D.
Research Institute for Brain and Blood Vessels-Akita
6-10 Senshukubota machi, Akita 010-0874  JAPAN
phone +81-18-833-0115 ext 769, fax +81-18-833-2104
E-mail: k...@akita-noken.jp 

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