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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.''
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Local CVS access: '''''IMPORTANT:''''' CVS no longer ships with OSX 10.7 (Lion) and higher. To get CVS working on later versions of Mac OSX follow the directions [[http://apple.stackexchange.com/questions/108240/cvs-on-os-x-mavericks|on this page]].
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Users who have an account at the Martinos Center can download the source code from the local CVS repository using the following commands:
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# Local access
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}}}
Remote CVS access:
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{{{ # Or, for remote access:
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If you want the ''stable'' brach use the following command: Users who do NOT have an account at the Martinos Center can first [[https://surfer.nmr.mgh.harvard.edu/opensourcereg.html|register to receive the password to the CVS repository]], and then download the source code using the following commands:
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cvs checkout -P -r stable5 dev cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
# Type in password

# 'Trunk' version (most up-to-date)
cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev

# 'Release 5.3' version
cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r release_5_3_0 dev
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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.''
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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: You will need to download and install gfortran, Qt4.7.4 and a prepackaged bundle of open-sourced libraries on your system.
 *[[http://gcc.gnu.org/wiki/GFortranBinaries#MacOS|gfortran]]
 *[[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]].
 *[[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt|open-source libraries]]

The download and install of gfortran and Qt is straight forward, just click the .dmg file. To install the prepackaged bundle of open-source libraries, execute the following command after downloading it:
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tar -C /usr/pubsw/packages -xzvf DownLoadedFileName.tar.gz tar -C /usr/pubsw/packages -xzvf DownloadedFileName.tar.gz
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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.''
'''''IMPORTANT:''''' Do to a Qt bug, after you install Qt you must delete line 320 from the file {{{/Library/Frameworks/QtCore.framework/Headers/qglobal.h}}} (Removing the line that says '#warning "This version of Mac OS X is unsupported"')
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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.) 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/USER/freesurfer}}}. Type the following commands in the top-level Freesurfer directory (the directory that contains configure.in and all the mri_* and mris_* directories.)
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      --prefix=/Users/zkaufman/freesurfer       --prefix=/Users/USER/freesurfer \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa
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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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      --prefix=/Users/zkaufman/freesurfer \
      --disable-GUI-build \		       --prefix=/Users/USER/freesurfer \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa \
      --disable-tcltk-apps \
      --with-qt=/usr/bin \
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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) 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

IMPORTANT: CVS no longer ships with OSX 10.7 (Lion) and higher. To get CVS working on later versions of Mac OSX follow the directions on this page.

Users who have an account at the Martinos Center can download the source code from the local CVS repository using the following commands: 

# Local 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

Users who do NOT have an account at the Martinos Center can first register to receive the password to the CVS repository, and then download the source code using the following commands: 

cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
# Type in password

# 'Trunk' version (most up-to-date)
cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev

# 'Release 5.3' version
cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r release_5_3_0 dev

2. Get the Libraries

You will need to download and install gfortran, Qt4.7.4 and a prepackaged bundle of open-sourced libraries on your system.

The download and install of gfortran and Qt is straight forward, just click the .dmg file. To install the prepackaged bundle of open-source libraries, execute the following command after downloading it: 

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

IMPORTANT: Do to a Qt bug, after you install Qt you must delete line 320 from the file /Library/Frameworks/QtCore.framework/Headers/qglobal.h (Removing the line that says '#warning "This version of Mac OS X is unsupported"')

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/USER/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/USER/freesurfer \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa
make -j4
make install

If your on Mac OSX 10.7 or 10.8 (Lion or Mountain Lion): 

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

make -j4
make install

Done!

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