Index

Contents

  1. Git Clone
  2. Building
  3. Adding a new binary to the tree
  4. Using Git

This page is targeted at Martinos Center users who wish to inspect, build or develop within the FreeSrufer code base. Non-Martinos users wishing to work with the FreeSrufer code base should consult the read-only git repo http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

1. Git Clone

First thing users at the Martinos Center will need to do is add the newer version of the git and git-annex software to their PATH environment variable. This should be added to the .cshrc or .bashrc file in the users home directory: 

## csh
$> setenv PATH /usr/pubsw/packages/git-annex/current/bin:$PATH

## bash
$> export PATH=/usr/pubsw/packages/git-annex/current/bin:$PATH

Users can then clone FreeSurfer repository as follows: 

## Get source code files (206 MB)
$> git clone file:///space/freesurfer/repo/freesurfer

1.1. Getting the Data Files

The FreeSurfer repository contains a large number of data files (pdfs, test data, etc) which are not normally included with a default git clone of the repo. Users who wish to clone the repository for the purposes of just inspecting source code and/or build the code, the git clone command from above is all that is required. Users who want to run build time checks, or perform a full local installation, or just want all the data files contained in the repository, will need to run the following command: 

## Change directories
$> cd freesurfer

## Get only the data files required for build time checks (1.9 GB)
$> git annex get --metadata fstags=makecheck .

## Get only the data files required for local installation (4.3 GB)
$> git annex get --metadata fstags=makeinstall .

## Just give me everything! Not Recommended (6.8 GB)
$> git annex get .

2. Building

2.1. Setup Configure

It is necessary to run a pre-configure script, to create the platform specific tools required by configure (execute in the freesurfer directory created by git clone). This script runs a set of commands (aclocal, libtoolize, automake v1.9.6, autoconf v2.59) that creates the platform specific files for configure and puts them in the 'fsdev/config' directory. 

$> ./setup_configure

2.2. Configure

Now you need to configure your building parameters for your machine by running the configure script. Users at the Martinos Center should for the most part be fine with the default settings, but the configure script does accept many options for pointing to specific libraries and other build specific parameters. One exception is if a user wants to perform a local installation of FreeSurfer, he/she should use the --prefix flag. Type ./configure --help for a full list of options. For example: 

## Default configuration
$> ./configure

## Specify an installation location
$> ./configure --prefix=~/freesurfer_install_dir

## See all possible options
$> ./configure --help

FreeSurfer builds against the following set of open-sourced libraries, which are installed under the /usr/pubsw/packages directory on all NMR computers:

All these packages will be found by default by the ./configure script. But there are options to specify where certain packages exists if a user wishes to build against a different version of one of the open-source libraries. For example: 

## Specify a specific version of qt
$> ./configure --with-qt=/usr/pubsw/packages/qt/4.8.5

2.3. Compile

You can now run 'make' to build the all individual programs in the FreeSurfer source tree. Binaries will automatically be placed in their individual subdirectories. 

$> make -j 4

Handy hint: the -j 4 option to make tells it to run four simultaneous make processes, which, if building on a multi-processor machine, can speed-up the build.

If you want to compile just one binary at a time, for example, if you are developing an app, than cd to the directory of the program you want and use 'make' to compile it: 

$> cd mri_info
$> make

This creates mri_info in the mri_info/ directory. However, be aware the many program depends on the existence of libraries having already been build like libutils. Therefore users will need to build a few of the library directories first (e.g. utils, fsgdf, xml2, etc).

2.4. Install

To install all binaries and support files into your private FreeSurfer installation, type 'make install' from the toplevel fsdev/ directory, like this: 

$> make install

This will create a local FreeSurfer installation in the directory specified by the --prefix option to configure scipt (see above). Note that if you do not specify this location, it will try to install to /usr/local, which will probably require root access.

Note that you can also run 'make release'. 'make install' makes and installs the NMR internal version of FreeSurfer, while 'make release' makes the public version which omits some stuff.

The first time you run 'make install', it will take a while to copy all the big data files to the new installation. Subsequent 'make installs' will only copy the changed files.

If you only want to install a single binary, run 'make install' from a subdirectory. For example, running 'make install' from the scuba/ directory will copy the scuba binary and its support script files to the proper locations. Running 'make install' from scripts/ will copy all the necessary scripts to the right location.

3. Adding a new binary to the tree

For this example we will assume you want to create a program called 'MYPROG' and want to add it to the FreeSurfer tree:

1) Make a directory called MYPROG under the freesurfer directory, and put your source code there. In the simplest case you will have a single source code file called MYPROG.c. 

## Create the MYPROG directory and 'cd' into it
$> mkdir MYPROG
$> cd MYPROG
## The MYPROG.c file goes here

2) Copy freesurfer/dummy/Makefile.am into MYPROG/ and customize it, replacing 'dummy' with 'MYPROG'. Also delete the notes that are there. Be sure to change: 

bin_PROGRAMS = MYPROG

3) Modify configure.in to add MYPROG/Makefile to the list of files in the definition of AC_OUTPUT (these are in roughly alphabetical order). 

## configure.in ##

AC_OUTPUT(
... <list of files> ...
MYPROG/Makefile
... <list of files> ...
)

4) Modify freesurfer/Makefile.am to add MYPROG to the MRISUBDIRS or MRISSUBDIRS definition. (You can also alternatively add it to the end of any of the *SUBDIRS categories.) 

## Makefile.am ##

MRISUBDIRS= \
... <list of files> ...
MYPROG \
... <list of files> ...

Once these 4 steps are complete MYPROG should automatically be built with the rest of FreeSurfer.

4. Using Git

FreeSurfer developers should run the following commands to get their git configuration settings set up properly. These commands only need to be run once: 

## User settings.
$> git config --global user.name "John Doe"
$> git config --global user.email johndoe@nmr.mgh.harvard.edu

## Some recommended configuration settings:
$> git config --global push.default current
$> git config --global color.ui true

4.1. Examples

In order to facilitate the transfer from CVS to Git, the following examples use terms like "checkout" and "branch". Generally these terms mean two different things when talking about CVS vs. Git, but for the following examples they can be thought of as similar concepts.

"Checkout" the main branch: 

$> git clone file:///space/freesurfer/repo/freesurfer master

"Checkout" the stable6 branch: 

$> git clone -b stable6 file:///space/freesurfer/repo/freesurfer

"Commit" a modified source code file: 

$> git commit -m "Added new capabilities." <file_name>
$> git push

Add a new source code file: 

$> git add <file_name>
$> git commit -m "Initial add of new file." <file_name>
$> git push

From the example above DevelopersGuide_git#Adding a new binary to the tree, if your program successfully builds/installs/runs and is thus ready to be checked into the repository, you can commit the files as follows: 

$> git add MYPROG/MYPROG.c MYPROG/Makefile.am
$> git commit -m "Initial add of MRPROG." MYPROG/MYPROG.c MYPROG/Makefile.am configure.in Makefile.am
$> git push

Additional information on how to use Git can be found on the Atlassian websites which has decent tutorials and examples to help users getting started with Git: https://www.atlassian.com/git/tutorials/saving-changes

4.2. Data Files and git-annex

Data files represent a special use-case, and they should not go into the normal Git repository. Instead git-annex is used to store all data files that are part of the FreeSurfer repository. Generally speaking, data files are anything not source code related - pdfs, compressed tarballs, test data, precompiled binaries, and image files are all examples of data files that should be stored in git-annex. Simple text files like Look-up tables and configuration files, while not exactly source code, are NOT considered data files. Those files CAN go in the normal repository.

Below are a few examples on how one would work with the git annex repository to modify or add new data files. But feel free to contact the !FreeSurfer administrator with any questions or concerns or may have.