Differences between revisions 1 and 2
⇤ ← Revision 1 as of 2013-03-29 11:13:33 →
Size: 2524
Editor: ZekeKaufman
Comment:
← Revision 2 as of 2013-03-29 11:19:18 → ⇥
Size: 2638
Editor: ZekeKaufman
Comment:
Deletions are marked like this. Additions are marked like this.
Line 23: Line 23:

If you want the ''stable'' brach use the following command:
{{{
cvs checkout -P -r stable5 dev
}}}
Line 26: Line 32:
Freesurfer builds against a set of open-sourced libraries. Special bundles of this open-source code are available on the [[http://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/|distribution site]]. Once you have downloaded the bundle, execute the following command to install them into the {{{/usr/pubsw/packages}}} directory: Freesurfer builds against a set of open-sourced libraries. Special bundles of this open-source code are available on the [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt|distribution site]]. Once you have downloaded the bundle, execute the following command to install them into the {{{/usr/pubsw/packages}}} directory:

Index

This page is targeted at those who wish to develop and build the freesurfer source code on their Mac OSX platform. These instructions have been tested for Mac 10.6 (Snow Leopard) and 10.7 (Lion).

Contents

  1. Get the Source Code
  2. Get the Libraries
  3. Set Your Path
  4. Setup, Configure, Make

1. Get the Source Code

If you already have a working local copy of the CVS repository then you can ignore this step.

Local CVS access: 

export CVSROOT=/space/repo/1/dev
cvs checkout -P dev

Remote CVS access: 

export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev
cvs checkout -P dev

If you want the stable brach use the following command: 

cvs checkout -P -r stable5 dev

2. Get the Libraries

If you are at the NMR Center and already have /usr/pubsw/packages mounted on your system then you can skip this step.

Freesurfer builds against a set of open-sourced libraries. Special bundles of this open-source code are available on the distribution site. Once you have downloaded the bundle, execute the following command to install them into the /usr/pubsw/packages directory: 

mkdir -p /usr/pubsw/packages
tar -C /usr/pubsw/packages -xzvf DownLoadedFileName.tar.gz

NOTE: You may install the open-sourced libraries into any directory you wish but it is best to install them into the /usr/pubsw/packages directory, as that is where Freesurfer setup script checks for its packages during its setup. If you choose to install in a different location than the onus will be on you to setup everything correctly during the configure phase. That is outside the scope of this document.

3. Set Your Path

export PATH=/usr/pubsw/packages/autotools/bin:$PATH

4. Setup, Configure, Make

Determine the location you want Freesurfer to be installed. For example, in case case we will assume the user wants freesurfer to be installed in /Users/zkaufman/freesurfer. Type the following commands in the top-level Freesurfer directory (the directory that contains configure.in and all the mri_* and mris_* directories.)

If your on Mac OSX 10.6 (Snow Leopard): 

./setup_configure
./configure \
      --prefix=/Users/zkaufman/freesurfer
make -j4
make install

If your on Mac OSX 10.7 (Lion): 

./setup_configure
./configure \
      --prefix=/Users/zkaufman/freesurfer \
      --disable-GUI-build \
      --with-Mac32-GUIs
make -j4
make install

Done!

Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu