Navigation(children)

Index

TableOfContents

1. CVS Checkout

You can checkout the FreeSurfer source code from the NMR center using local CVS access or remotely by using SSH as the CVS remote connection method.

1.1. Local CVS Access

The CVS repository is /space/repo/1/dev. Use this as your CVSROOT. You can either set it as an environment variable:

setenv CVSROOT /space/repo/1/dev

or specify it in the checkout command with the -d option. Note that the CVS root is cached in a CVS checkout directory, so if you choose to use the -d method, you will only have to do it once during your first checkout.

Check out the code with the CVS checkout command. The archive name is dev.

cvs checkout -P dev

or

cvs -d /space/repo/1/dev checkout -P dev

This will copy the entire archive to your directory, creating a directory called dev/. The -P option will purge the old directories that have been removed from the CVS repository.

Generally it is handy to define an environment variable called FSDEV which is set to your Freesurfer development directory. Be sure also to define your FREESURFER_HOME environment variable set to the intended Freesurfer installation directory.

1.2. Remote CVS Access

Tell CVS to use SSH to access the archive by setting the following environment variable:

setenv CVS_RSH ssh

Use the following string as your CVS root:

setenv CVSROOT :ext:USER@MACHINE.nmr.mgh.harvard.edu:/space/repo/1/dev

Where USER is your username and MACHINE is one of the NMR machines visible to the outside, i.e. gate, entry, or door. Then use the CVS commands normally.

Note that using this method makes an SSH connection for every CVS command, and you will be required to enter your password every time. You may want to look into a utility to automatically authenticate SSH connections, such as SSH agent. See:

http://mah.everybody.org/docs/ssh

When working in a CVS checkout directory, cvs knows where the CVSROOT is for that directory. However, it doesn't know what CVS_RSH method to use, so if you are grabbing files remotely, you may want to set this in your login file.

2. Running configure

Prior to running the configure script, the following is necessary to create the platform specific tools required by configure (execute in the dev/ directory):

  ./setup_configure

This script runs a set of commands (aclocal, libtoolize, automake, autoconf) that creates the platform specific files for configure and puts them in the 'dev/config' directory.

Now you need to configure your building paramters for your machine:

  ./configure

This runs the configure script which checks a bunch of local settings and libraries that are needed. You will probably need to supply some extra options:

--prefix=~/work/freesurfer

The prefix option determines where your build will be installed when you use the 'make install' command. This is your private copy of FreeSurfer, not a release for others, so put it in your own directory space.

--with-mni-dir=/usr/pubsw/packages/mni/current --with-tcl-dir=/usr/pubsw/packages/qt/current

These options specify where certain packages are. These are often needed so configure can find libraries installed in /usr/pubsw. Note that you should have /usr/pubsw mounted on your machine. This is normal for NMR computers.

Freesurfer builds against the following set of open-sourced libraries, thus, these must be installed prior to building:

• GSL JPEG TIFF Tcl 8.4 Tk 8.4 Tix 8.4 BLT GLut Qt 3.3.4

Freesurfer also builds against certain packages of the MINC toolkit. A special bundle of the source code for the packages require by Freesurfer has been put together and is available on the download site:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/

Look for mni.srcbuild.tar.gz, and mni.srcbuild.README.txt describes the build process.

  CFLAGS=-I/sw/include
  CXXFLAGS=-I/sw/include
  LDFLAGS=-L/sw/lib

The above are needed on Macs on which software is installed in /sw by fink or FinkCommander. Note that you can also use these options to specify other compile-line flags. Note that these options aren't preceded by dashes.

--with-tixwish=/usr/sw/bin/tixwish8.1.8.4

This one is also often needed for Macs.

A sample configure line for the Mac:

  ./configure --prefix=~/home/freesurfer \
        CFLAGS=-I/sw/include \
        CXXFLAGS=-I/sw/include \
        LDFLAGS=-L/sw/lib \
        --with-mni-dir=/usr/local/mni \
        --with-tixwish=/usr/sw/bin/tixwish8.1.8.4

3. Building

You can now run 'make', edit and build code, etc. The first thing you should do is 'make' to build libraries like libutils. (Note that all libs will be built to your local checkout directory.) To just build libutils, cd into utils/ and run make.

You can now compile individual programs or all of them at once. To compile all of them, just run 'make' from dev/. Binaries will automatically be placed in their individual subdirectories.

However you may just want to compile one of them at a time. To do so, 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.

3.1. Adding a new binary to the tree

Assuming that you have a source file MYPROG.c that compiles into MYPROG and want to add it to the FreeSurfer tree:

1) Make the directory in dev and copy the source file there. Name the directory MYPROG and the source file MYPROG.c.

mkdir dev/MYPROG
cp MYPROG.c dev/MYPROG

2) Tell the autotools to build your program when you type make from the top dir.

a) Modify dev/configure.in to add MYPROG/Makefile to the list at the end of the file in the definition of AC_OUTPUT. Be sure to add a backslash at the end of line:

AC_OUTPUT( \
... other files ...
MYPROG/Makefile \
)

b) Modify dev/Makefile.am to add MYPROG to the SUBDIRS definition. (You can also alternatively it to the end of MRISUBDIRS or MRISSUBDIRS if more appropriate.)

SUBDIRS= ... other directories ... MYPROG

c) Copy dev/dummy/Makefile.am into MYPROG/ and customize it, replacing 'dummy' with 'MYPROG'. Be sure to change:

bin_PROGRAMS = MYPROG

d) Copy in the additional testing file dev/dummy/myown.c. You can customize it for your test program later.

3) Run automake from dev/. You should get no errors. If you do, make sure you followed the above instructions properly. Also try the AutoconfTroubleshooting page. Verify that this stepped work by checking if MYPROG/Makefile.in was created.

4) Run autoconf to generate a new configure script that now includes your new MYPROG directory.

5) Run ./configure with the parameters you previously used. To check these out, run head config.log from dev/. The output should include the ./configure line you used. Copy it, but leave out the --no-create --no-recursion options if present.

[dev/]$ head config.log
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by Freesurfer configure 0.1, which was
generated by GNU Autoconf 2.57.  Invocation command line was

  $ ./configure --with-mni-dir=/usr/pubsw/packages/mni/current --prefix=/home/kteich/freesurfer/dev --no-create --no-recursion

## --------- ##
## Platform. ##
[dev/]$ ./configure --with-mni-dir=/usr/pubsw/packages/mni/current --prefix=/home/kteich/freesurfer/dev

Note: Do not just copy this example, use what's in your own config.log file!

6) Run make and verify that your binary program MYPROG/MYPROG was created.

7) Check in your changes.

[dev/] cvs ci -m "Added MYPROG" configure configure.in Makefile.am Makefile.in
[dev/] cvs add MYPROG
[dev/] cd MYPROG
[MYPROG/] cvs add Makefile.am Makefile.in MYPROG.c myown.c
[MYPROG/] cvs commit -m "First checkin." Makefile.am Makefile.in MYPROG.c myown.c

4. Installing

To install all binaries and support files into your private FreeSurfer, use 'make install' from the toplevel dev/ directory. This will make a directory called freesurfer/ in the directory specified by the --prefix option to configure, above. Note that if you do not specify this location, it will try to install to /usr/local, which you probably don't have permission to do. Even if you do, i.e. you are installing on a laptop, it's generally better to specify a prefix of /usr/local/freesurfer to keep everything in the same place.

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.

4.1. autoconf Troubleshooting

Here's a list of common problems and solutions for autotools problems:

[AutoconfTroubleshooting]

4.2. Making changes live

The current setup allows you to have your own private installation of FreeSurfer using configure --prefix=/your/private/directory. This lets you use make install to easily install the entire FreeSurfer environment into a local copy.

The purpose of having your own private installation of FreeSurfer is to use it as a testbed to make sure that (1) your updates, whatever they be, work in freesurfer/ setup that is just like a real one, and (2) your updates are properly installed using 'make install' and 'make release'. Once you are sure of these two things, check in your updated files, including any Makefile.am and Makefile.in changes, etc, and the nightly build script will take care of the rest.

The nightly build stuff automatically updates and installs the dev/ distribution on all seven build platforms. The next morning, just check if your changes are in any /usr/local/freesurfer/dev; if not, notify me. If they are in one /usr/local/freesurfer, they will be in the rest of them. (If any build/installs fail, I am notified, and will do the build/install manually for that day.)

Things not to do:

- Don't test your local setup by manually copying files into your local freesurfer/. Otherwise you can't be sure that the automated build will correctly install your files with 'make install' and 'make release'. The only way files should get into your freesurfer/ distro as with 'make install' and 'make release'.

- Don't try to install into /usr/local/freesurfer yourself (i.e. by setting your .configure --prefix=... to target it). It's set up so the build scripts can do their job automatically. Also, you would only be installing on one of the seven platforms. It's a pain to do all three builds on all build machines and verify it all worked - that's what the nightly build script is for, so let it do it for you.

If you absolutely need a 'hot fix' right away, and need to make changes live in any of the /usr/local/freesurfers before the nightly build stuff goes, let KevinTeich know and he'll do it.

4.3. How the nightly build works

First a note on the directory structure. In /space/freesurfer/build there is a directory for each build machine. Each builds a platform in /space/freesurfer, i.e. /space/freesurfer/rh9. Currently these are as follows:

Inside each /space/freesurfer/build/MACHINE is trunk/ and stable/, as well as directories for local Qt installs, and on Tiger, MNI, and files for automated building. configure_options.txt contain command-line arguments for configure for that platform, and source_before_building.csh (optional) contains environment variables that must be set (mainly things like CPPFLAGS that are used by configure but can't be passed in to configure via the command line from a cronjob). The trunk and stable directories contain cvs checkouts.

In /space/freesurfer/build/scripts is build_dev.csh and build_betapub.csh. Each build machine runs build_dev.csh nightly. It basically goes to /space/freesurfer/build/MACHINE/trunk/dev and does the following:

cvs update -d
make distclean
rm -rf autom4te.cache
aclocal
autoconf
automake
./configure  `cat ${BUILD_DIR}/configure_options.txt` --prefix=/usr/local/freesurfer/dev
make
rm -rf freesurfer/bin_old
mv freesurfer/bin freesurfer/bin_old
make install

The build_betapub.csh works in /space/freesurfer/build/MACHINE/stable/dev and also does:

make release prefix=/usr/local/freesurfer/pub

All the autotools stuff gaurantees that enough of the Makefiles will be regenerated to ensure that new directories will be added to all Makefiles. This wouldn't normally be done with a simple ./config.status because configure may need to be regenerated to know about new directories.

Currently (as of 4/8/2005) the build_betapub.csh script is not run regularly. This is to minimize interruption to the freesurfer/beta build.

Note that all machines can run these scripts at any time from the command line. This lets maintainers (KevinTeich and NickSchmansky) explicity do a build and install on any machine if a 'hot fix' is needed.

Additionally, a developer can go to each machine's /space/freesurfer/build/MACHINE/trunk/dev, update code, and do a make install from an individual binary directory if a hot fix is needed for a single binary before the nightly build. This is the quick and dirty way of doing an update for a single binary without waiting for the nightly build. For example, to update tkmedit, the developer would, for each build machine:

cd /space/freesurfer/build/MACHINE/trunk/dev/tkmedit
cvs update
make install

This would install the files to /usr/local/freesurfer/dev. However, the developer must know about file dependencies. In this case, the script files that tkmedit may also need to be updated, so the developer would also have to cvs update and make install from dev/scripts.

5. RPM

See RpmInfo

6. Medical Image Format FAQ

[http://www.dclunie.com/medical-image-faq/html Medical Image Format FAQ]