Index

TableOfContents

This page is targeted at those who have access to the FreeSurfer source code, and wish to build this source code on their own Unix platform (whether it be an NMR Martinos Center platform, which has all required libraries, or on some arbitrary Unix platform, where the dependent libraries must be installed prior to building FreeSurfer).

1. CVS Checkout

If you have an NMR account, 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.

Internal to the NMR Center, there exists a [http://minerva:8080 CVSweb server] with [http://minerva:8080/cgi-bin/cvshistory.cgi CVShistory].

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 ('door', not 'gate'). Then use the CVS commands normally.

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

cvs checkout -P dev

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. Open Source Distribution

not available just yet

3. Configuring

While not strictly necessary, NMR center developers are encouraged to run a pre-configure script, to create the platform specific tools required by configure (execute in the dev/ directory created by cvs checkout): 

./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. Those who are working with the open-source distribution should not need to run this script, as the default files should work for most platforms, but ./setup_configure is there if someone is having autoconf issues.

Now you need to configure your building parameters 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. Generally, a developer will set their $FREESURFER_HOME to their working directory (in this case FREESURFER_HOME is ~/work/freesurfer). Note: Do not install freesurfer in the same directory as the source. In-source building is not supported.

If you are compiling in the NMR Center, pass the option:

--enable-nmr-install

This will look for and install some files that are only usable in the Center. These files are not included in external (open-source) release, so using this option on an external release will result in an error as required files will not be found.

There are options to specify where certain packages exist, such as: --with-mni-dir=/usr/pubsw/packages/mni/current 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:

If these libraries are not available on your system, then they must be built and installed. Special bundles of this open-source code are available on the distribution site:

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

Also in this 'bundle' directory is a Linux script called 'fs_lib_check' which will check your system for these libraries given some prior sysadmin installation. If you do not have a set of libs, then in the src directory are the .tar.gz files containing the open-source code from which they can be built. The files tcltktixblt.tar.gz, tiffjpegglut.tar.gz, and mni-1.4-srcbuild.tar.gz each contain special build scripts that perform the work of building and installing these libraries. Refer to those scripts (with 'build_' in the filename preface) to see what they do. The VXL and VTK source requires cmake to build. Refer to the [http://vxl.sourceforge.net VXL home page] and the notes below for build instructions. For the simplest installation, it is recommended to install these packages in a directory called /usr/pubsw/packages, as the Freesurfer setup script checks for this directory for its packages during its setup. Here is a table of recommended installation paths and build notes for the 3rd-party packages:

Suggested install path:

Source bundle:

Build notes:'

/usr/pubsw/packages/mni/current

mni-1.4-srcbuild.tar.gz

attachment:README-MNI-MGH.txt

/usr/pubsw/packages/vxl/current

vxl-1.8.0.tgz

attachment:README-VXL-MGH.txt

/usr/pubsw/packages/vtk/current

vtk-5.0.2.tar.gz

attachment:README-VTK-MGH.txt

/usr/pubsw/packages/tcltktixblt/current

tcltktixblt-8.4.6.tar.gz

see build_tcltktixblt.csh

/usr/pubsw/packages/tiffjpegglut (Mac OS X only)

tiffjpegglut-1.1.tar.gz

see build_tiffjpegglut.csh

Freesurfer also builds against certain packages of the MINC toolkit. A special bundle of the MINC toolkit source code for the MINC packages required by Freesurfer has been assembled at MGH and is available from the download site:

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

Look for mni-1.4-srcbuild.tar.gz, and mni.srcbuild.README.txt describes the build process.

You will also need the following tools, with the listed version, or newer:

The source for these tools can be found in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs.

A sample configure line for a Linux machine at the NMR center having appropriate NFS mount-points (ie. /usr/pubsw/packages): 

./configure \
        --enable-nmr-install \
        --prefix="$FREESURFER_HOME" \
        --with-mni-dir="/usr/pubsw/packages/mni/current" \
        --with-vxl-dir="/usr/pubsw/packages/vxl/current" \
        --with-vtk-dir="/usr/pubsw/packages/vtk/current" \
        --with-tixwish="/usr/pubsw/packages/tcltktixblt/current/bin/tixwish8.1.8.4" \
        --with-tcl-dir="/usr/pubsw/packages/tcltktixblt/current"

A sample configure line for a Mac OS X machine at the NMR center having appropriate NFS mount-points (ie. /usr/pubsw/packages): 

./configure \
        --enable-nmr-install \
        --prefix="$FREESURFER_HOME" \
        --with-mni-dir="/usr/pubsw/packages/mni/current" \
        --with-vxl-dir="/usr/pubsw/packages/vxl/current" \
        --with-vtk-dir="/usr/pubsw/packages/vtk/current" \
        --with-tcl-dir="/usr/pubsw/packages/tcltktixblt/current" \
        --with-tixwish="/usr/pubsw/packages/tcltktixblt/current/bin/tixwish8.1.8.4" \
        --with-pkgs-dir="/usr/pubsw/packages/tiffjpegglut" \
        --with-glut-dir="/usr/pubsw/packages/tiffjpegglut" \
        --with-gl-dir="/usr/X11R6"

Before attempting to build and install the 3rd-party packages from source, it is recommended to just start by running: 

./configure  \
        --enable-nmr-install \
        --prefix="$FREESURFER_HOME"

and observe the errors. configure will tell you which packages are already installed on your system. Read the file config.log, generated by configure, for error messages. Don't include the --enable-nmr-install option if building using an open-source distribution, as that distribution doesnt contain the nmr specialties.

Be aware that the tcl/tk/tix/blt combo is particularly tricky. While many systems have tcl/tk installed, the tricky thing is getting tix and BLT to work with tcl/tk. Thus, our installation package (tcltktixblt.tar.gz) is the easiest route to successfully getting these four guys to work together. Also, if the --with-tcl-dir=DIR option is not included in the configure command, then the Tcl/Tk apps (tkmedit, tksurfer, tkregister, scuba and orient_mri) are not built. This handy if these GUI apps are not required (such as for a cluster machine).

4. 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. Like this: 

cd dev
make -j 9

Handy hint: the -j 9 option to make tells it to run nine simultaneous make processes, which, if building on a multi-processor machine, can speed-up the build.

You may just want to compile one binary at a time, for instance, if you are developing an app. 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.

5. 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: 

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

SUBDIRS= ... other directories ... MYPROG

bin_PROGRAMS = MYPROG

and also delete the notes that are there.

3) Run ./set_configure from dev/. This runs aclocal, autoconf and automake. You should get no errors. If you do, make sure you followed the above instructions properly. Also try the AutoconfTroubleshooting page. Verify that this step worked by checking if MYPROG/Makefile.in was created.

4) Run ./configure with the parameters you previously used. To check these out, run head config.log from dev/, assuming you have run configure successfully on some prior occasion. 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 dev3, which was
generated by GNU Autoconf 2.59.  Invocation command line was

  $ ./configure --prefix=/space/minerva/1/users/nicks/freesurfer \
--with-mni-dir=/usr/pubsw/packages/mni/current \
--with-vxl-dir=/usr/pubsw/packages/vxl/current \
--with-tcl-dir=/usr/pubsw/packages/tcltktixblt/current \
--with-tixwish=/usr/pubsw/packages/tcltktixblt/current/bin/tixwish8.1.8.4

## --------- ##
## Platform. ##
[dev/]$ /configure --prefix=/space/minerva/1/users/nicks/freesurfer \
--with-mni-dir=/usr/pubsw/packages/mni/current \
--with-vxl-dir=/usr/pubsw/packages/vxl/current \
--with-tcl-dir=/usr/pubsw/packages/tcltktixblt/current \
--with-tixwish=/usr/pubsw/packages/tcltktixblt/current/bin/tixwish8.1.8.4

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

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

6) Check in your changes (note: do not commit Makefile.in, only Makefile.am is necessary). 

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

6. Installing

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

cd dev
make install

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.

7. Using CVS

When you want to commit your changes, use the cvs commit command. However, you must first check to see if the file(s) in the archive have changed since the last time you checked them out. To do so, run the cvs update command on the files you have changed. The -P option will purge (remove) files that have been removed from the CVS. 

cvs update -P

If any have changed, you will see the letter U followed by the file name. 

U myFile.c

This means somebody else committed a newer version of the file, and your copy was just updated.

If you and somebody else have made changes on the same file that conflict each other, you will see the letter C along with a message about the conflicts. 

C myFile.c

If the message states the conflicts have been resolved, you don't have to worry: cvs has merged the differences properly. If it says it couldn't merge the differences, you need to open the file in question, search for the string >>>, and merge the differences yourself.

Once the up to date check has been performed, you can commit your changes. If you are in a directory and want to commit all the files in that directory that you have changed, just use: 

cvs commit

This will commit changes in the current directory and any subdirectories. If you want to commit only certain files, use: 

cvs commit <filename>

Or you can only commit the code in the current directory with the -l switch: 

cvs commit -l

Each time, an editor will open and ask you to enter a log message. To bypass this, use the -m option and enter your log message on the command line: 

cvs commit -m "some descriptive changelog comment" <filename>

A synonym for commit is ci, so you can just: 

cvs ci -m "fixed stuff" <filename>

Periodically, you should update your working copy to be in sync with the archive. CVS will look at all your files and see if the ones in the archive are different. If so, it will update your copy. CVS will not delete local modifications you have made. To do this update: 

cvs update -d -P

The -d switch adds any new directories and is not strictly necessary, but is a good habit, because if you don't use it you will update existing files but will now add new directories. The -P option purges directories of files that have been removed in the past.

Similarly, you can update an entire directory or a single file. To commit all the code in the current directory (code that has not been changed will not be commited): 

cvs ci -m "fixed many things"

To restore an edited version to the version in the archive, either delete the file and cvs update, and the archive version will be copied to the local work area, or use the -C option to cvs update to replace your copy with one from the archive.

To add a new file to the archive, use the add command and then commit the file: 

cvs add <filename>
cvs commit -m "added the file" <filename>

To remove a file, remove in cvs and locally (with the -f flag), and commit: 

cvs remove -f <filename>
cvs commit -m "removed the file" <filename>

That covers most of the CVS commands you'll have to to use.

Additional stuff:

To tag a group of code with a text label: 

cvs tag alpha-1

To retrieve a tagged group of code: 

cvs update -r alpha-1

There are more useful commands, but these are the most commonly used ones. See http://www.cvshome.org for more info.

For more info on CVS, check out www.cvshome.org or the CVS man pages.

Summary:

check in a file 

cvs commit

get newest versions. merges newer versions than the ones you had with your working versions. 

cvs update -A

tag working files: 

cvs tag -c tag-name

if any working copies are edited, will report an error. check in first.

checkout a tag: 

cvs checkout -r tag-name archive

split off a branch based on current revisions in working copy: 

cvs tag -b branch-name

note: doesn't make working copy the branch.

split off a branch: 

cvs rtag -b -r tag-name branch-name archive

check out a branch: 

cvs checkout -r branch-name archive

switch working copy to a branch: 

cvs update -r branch-name archive

-or- 

BCD archive; cvs update -r branch-name

to find out what branch the working copy is on: 

cvs status

look for sticky tag field.

join the changes in a branch to current working copy: 

cvs update -j branch-to-join file

best to tag merged branches after every merge.

joing the changes in a revision to current working copy: 

cvs update -j rev file

i.e. two people check out 1.3, someone checks it in 1.4, you try to check it in and get a conflict, can join in the changes with cvs update -j 1.4 file.c

add a new file: 

cvs add file; cvs commit file

remove a file (but keep in older revisions): 

rm file; cvs remove file; cvs commit file

rename a file: 

mv old new; cvs remove old; cvs add new; cvs commit old new

To receive an email notification about any file that has been commited by somebody else: 

cd dev
cvs watch add

To undo this, and disable receiving an email notification about files that have been commited, type: 

cd dev
cvs watch remove

See also: [http://www.psc.edu/~semke/cvs_branches.html CVS Branch and Tag Primer] and [http://badgertronics.com/writings/cvs/keywords.html CVS Keywords]

8. Troubleshooting autoconf issues

[wiki:AutoconfTroubleshooting Here's a list of common problems and solutions for autotools problems.]

9. Martinos Center issues

see [wiki:DevelopersGuide/MartinosCenter Martinos Center issues] page

10. Coding Guide

This page deals specifically with coding issues.

[wiki:DevelopersGuide/CodingGuide CodingGuide]