Readme

Compile FreeSurfer on ppc64.

Using the docker container in this repo, which compiles itk 4.13 from source and mostly following along here with minor modifications to the FreeSurfer dev branch which

• disable the compilation of mri_watershed
  • this is the only binary that includes affine.hpp which seems hard coded to x86
• diabled staticlly linking of fortran binaries
  • hard coded for now, ideally this would be a cmake option that can be set independently of architecture

Build container

make

It gets tagged as fs-src

Setup

mkdir ~/fs
cd ~/fs
mkdir bin
git clone git@github.com:pwighton/freesurfer.git
cd freesurfer
git checkout 20191115-ppc64

TODO: get the Freesurfer git annex data (this will compile and install, recon-all wont run without it.

Jump into the container

docker run -it --rm -v ~/fs:/fs fs-src /bin/bash

Then build FreeSurfer. Might have to tweak:

• -DGFORTRAN_LIBRARIES="/usr/lib/gcc/ppc64le-redhat-linux/4.8.2/libgfortran.so"

cd /fs/freesurfer
rm -f ./CMakeCache.txt
cmake . \
  -DBUILD_GUIS=OFF \
  -DMINIMAL=ON \
  -DMAKE_BUILD_TYPE=Release \
  -DINSTALL_PYTHON_DEPENDENCIES=OFF \
  -DDISTRIBUTE_FSPYTHON=OFF \
  -DCMAKE_INSTALL_PREFIX="/fs/bin" \
  -DFS_PACKAGES_DIR="/usr" \
  -DPPC64=ON \
  -DCMAKE_CXX_FLAGS="-DPPC64" \
  -DCMAKE_C_FLAGS="-DPPC64" \
  -DGFORTRAN_LIBRARIES="/usr/lib/gcc/ppc64le-redhat-linux/4.8.2/libgfortran.so"
make -j 4
make install