| Deletions are marked like this. | Additions are marked like this. |
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export CVSROOT=/space/repo/1/dev cvs checkout -P dev |
$> export CVSROOT=/space/repo/1/dev $> cvs checkout -P dev |
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export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev cvs checkout -P dev |
$> export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev $> cvs checkout -P dev |
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| xcode-select --install | $> xcode-select --install |
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sudo port install gcc44 cd /opt/local/bin sudo ln -s gcc-mp-4.4 gcc sudo ln -s g++-mp-4.4 g++ |
$> sudo port install gcc44 $> cd /opt/local/bin $> sudo ln -s gcc-mp-4.4 gcc $> sudo ln -s g++-mp-4.4 g++ |
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curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/mountain_lion/MacOSX_Lion_Packages.tar.gz sudo mkdir -p /usr/pubsw/packages sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz |
$> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/mountain_lion/MacOSX_Lion_Packages.tar.gz $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz |
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| export PATH=/usr/pubsw/packages/autotools/bin:$PATH | $> export PATH=/usr/pubsw/packages/autotools/bin:$PATH |
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./setup_configure ./configure --disable-Werror --prefix=/home/USER/freesurfer make -j4 make install |
$> ./setup_configure $> ./configure --disable-Werror --prefix=/home/USER/freesurfer $> make -j4 $> make install |
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/* ------- ------ ----- ---- ## page was renamed from freesurfer_mac_developers page #pragma section-numbers on 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 OSX 10.6, 10.7, and 10.8 (Snow Leopard, Lion, and Mountain Lion). As of the writing of this document, a build on OSX 10.9 (Mavericks) has not been completed. In order to build Freesurfer, the following prerequisite software will need to be installed on your OSX system: *[[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/qt-mac-opensource-4.7.4.dmg|Qt 4.7.4]] *[[http://gcc.gnu.org/wiki/GFortranBinaries#MacOS|gfortran 4.8.2]] *[[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] *[[https://developer.apple.com/xcode/|Xcode]] (and Command Line Tools) ##* Xcode 4.x Command Line Tools ([[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/xcode462_cltools_10_76938260a.dmg|Lion]], [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/xcode462_cltools_10_86938259a.dmg|Mountain Lion]]) '''''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"') ## '''''IMPORTANT:''' CVS no longer ships with OSX 10.8 Command Line Tools 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]].'' <<TableOfContents(3)>> === Get the Source Code === ==== (Martinos Users) ==== 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 }}} ==== (non Martinos Users) ==== 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 Read-only 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 cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev }}} === Get the Libraries === You will need to download and install the prepackaged bundle of open-sourced libraries ([[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/snowleopard/MacOSX_SnowLeopard_Packages.tar.gz| Snow Leopard]], [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/mountain_lion/MacOSX_Lion_Packages.tar.gz| Lion, Mountain Lion]]) on your system. To install the prepackaged bundle of open-source libraries, execute the following command after downloading it: {{{ curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/mountain_lion/MacOSX_Lion_Packages.tar.gz mkdir -p /usr/pubsw/packages tar -C /usr/pubsw/packages -xzvf MacOSX_*_Packages.tar.gz }}} === Set Your Path === {{{ export PATH=/usr/pubsw/packages/autotools/bin:$PATH }}} === Setup, Configure, Make === Type the following commands in the top-level Freesurfer directory. If your on Mac OSX 10.6 (Snow Leopard): {{{ cd dev ./setup_configure ./configure \ --prefix=<install-dir> \ --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.0_Cocoa make -j4 make install }}} If your on Mac OSX 10.7 or 10.8 (Lion or Mountain Lion): {{{ cd dev ./setup_configure ./configure \ --prefix=<install-dir> \ --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa make -j4 make install }}} Done! -------- === Troubleshooting === * If you are building the '''5.3 release''' than you will need to do the following: ### * Add [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/unwarpGradientNonlinearity.c|unwarpGradientNonlinearity.c]] to the {{{dev/utils}}} directory. ### * Add [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/unwarpGradientNonlinearity.h|unwarpGradientNonlinearity.h]] to the {{{dev/include}}} directory. -------- Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu */ |
This page is targeted at those who wish to develop and build the freesurfer source code on their OSX platform. These instructions have been tested for OSX 10.9 (Mavericks).
Contents
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
Or, you can get readonly CVS access to the source code by following the directions on this page:
2. Download and Install the Libraries
In order to build Freesurfer, the following prerequisite software will need to be downloaded and installed on your OSX system:
After you install Qt, you must delete line 320 from the file /Library/Frameworks/QtCore.framework/Headers/qglobal.h, the line that says "#warning "This version of Mac OS X is unsupported""
MacPorts (for installing gcc)
XQuartz 2.7.5 (OSX versions 10.9 and lower) or XQuartz 2.7.6 (OSX versions 10.10 and higher)
Install Xcode Command Line Tools:
$> xcode-select --install
Install gcc v4.4.7:
$> sudo port install gcc44 $> cd /opt/local/bin $> sudo ln -s gcc-mp-4.4 gcc $> sudo ln -s g++-mp-4.4 g++
Download and install the prebuilt package of open-source libraries:
$> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/mountain_lion/MacOSX_Lion_Packages.tar.gz $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz
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 /home/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.)
$> ./setup_configure $> ./configure --disable-Werror --prefix=/home/USER/freesurfer $> make -j4 $> make install
Done! Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu