Note: if this is your first time transitioning from an automake configuration, you might need to run make clean before building with cmake. So, assuming you have a freesurfer repository stored in ~/dev/freesurfer (and you're developing on the Martinos filesystem), you could set up a simple in-source build with: A build can be configured in the working directory by running cmake . The makefile also contains some notes on what packages to install for the different OS's in order to build freesurfer, though what you may need to install will vary depending upon how your machine has already been setup.ĬMake replaces the setup_configure and configure build steps in the automake build. For the Mac, if you do not have Homebrew installed under the standard path /usr/local, it will try to create a minimal install for you under. install (install location for freesurfer after build) will all be created in the subdirectory where makefile.wiki is. packages (location of downloaded 3rd party packages), and. Note that the Mac build uses the native clang compilers again (instead of gcc from homebrew). The last update to makefile.wiki was on building the freesurfer dev branch on: MacOS 10.15, CentOS 7 Ubuntu 18. This makefile will try to download a prebuilt set of third party packages so as not to reference /usr/pubsw from the Martinos Center in-house network, i.e., "build on an airplane" where everything is built from your local disks. (Alternately just use "make -f makefile.wiki"). Type "make" or "make help" after downloading the file makefile.wiki and renaming it from makefile.wiki to makefile. It has preset options for the cmake command for the different OS's, with targets to checkout/update the freesurfer source tree and run build/install targets. You can try using this makefile to run a cmake command, build and install freesurfer on CentOS and Ubuntu linux flavors as well as MacOS. Wget $version/cmake-$version.$Ĭomplete Cmake Build with makefile wrapper If you don't have /usr/pubsw/bin, you can follow If it's not in your path already, add the following to your. Unfortunately, /usr/bin/cmake is quite old, so you'll have to use /usr/pubsw/bin/cmake. The freesurfer cmake scripts require cmake 3.5 or greater.
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