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## page was renamed from freesurfer_mac_developers page
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'''Index'''
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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). 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) and 10.8 (Mountain Lion).
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''If you already have a working local copy of the CVS repository then you can ignore this step.'' ''If you already have a working local copy of the CVS repository then you can skip this step.''
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Local CVS access:
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# Local CVS access:
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}}}
Remote CVS access:
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{{{ # Or for remote access:
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''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 [[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:		 If you are at the NMR Center and already have {{{/usr/pubsw/packages}}} mounted on your system then you can skip this step. Otherwise, you are going to need to download and install a bundle of open-sourced libraries from 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 on your machine:
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'''''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.''
'''''NOTE:''' If you are building on a Lion or Mountain Lion platform (OSX 10.7 or 10.8) you MUST install qt4.7.4 on your system. This is an unfortunate consequence related to difficulties in building against the compiled version of Qt. Click the following link to download [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/qt-mac-opensource-4.7.4.dmg|qt-mac-opensource-4.7.4.dmg]] and install.''

You will also need gfortan. If this is not on your system, you can download it from here http://gcc.gnu.org/wiki/GFortranBinaries#MacOS
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If your on Mac OSX 10.7 (Lion):
If your on Mac OSX 10.7 or 10.8 (Lion or Mountain Lion):
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      --disable-GUI-build \
      --with-Mac32-GUIs		       --disable-tcltk-apps \
      --with-qt=/usr/bin \
      --with-Mac32-GUIs \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa

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) and 10.8 (Mountain 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 skip this step. 

# Local CVS access:
export CVSROOT=/space/repo/1/dev
cvs checkout -P dev

# Or for remote access:
export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev
cvs checkout -P 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. Otherwise, you are going to need to download and install a bundle of open-sourced libraries from the distribution site. Once you have downloaded the bundle, execute the following command to install them into the /usr/pubsw/packages directory on your machine: 

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

NOTE: If you are building on a Lion or Mountain Lion platform (OSX 10.7 or 10.8) you MUST install qt4.7.4 on your system. This is an unfortunate consequence related to difficulties in building against the compiled version of Qt. Click the following link to download qt-mac-opensource-4.7.4.dmg and install.

You will also need gfortan. If this is not on your system, you can download it from here http://gcc.gnu.org/wiki/GFortranBinaries#MacOS

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 or 10.8 (Lion or Mountain Lion): 

./setup_configure
./configure \
      --prefix=/Users/zkaufman/freesurfer \
      --disable-tcltk-apps \
      --with-qt=/usr/bin \
      --with-Mac32-GUIs \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa
make -j4
make install

Done!

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