|
Size: 2838
Comment:
|
Size: 3046
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| ## page was renamed from freesurfer_mac_developers page | |
| Line 3: | Line 2: |
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). |
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 OS X 10.7, 10.9 (Lion and Mavericks). |
| Line 7: | Line 4: |
| Line 10: | Line 6: |
| {{{ # 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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS|on this page]]: Or, you can use the super secret git repo which mirrors the CVS repo: |
|
| Line 12: | Line 20: |
| # Local CVS access: export CVSROOT=/space/repo/1/dev |
$> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git }}} |
| Line 15: | Line 23: |
| # Remote CVS access: export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev |
=== 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: * [[https://download.qt.io/archive/qt/4.7/qt-mac-opensource-4.7.4.dmg|Qt 4.7.4]] * [[http://gcc.gnu.org/wiki/GFortranBinaries#MacOS|gfortran 4.8.2]] * [[https://www.macports.org/install.php|MacPorts]] (for installing gcc) * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (OSX versions 10.9 and lower) * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (OSX versions 10.10 and higher) ''IMPORTANT: 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""''. Next, install Xcode Command Line Tools my typing the following on the command line: {{{ $> xcode-select --install }}} After Xcode has been installed, we need to install gcc v4.4.7 using MacPorts: {{{ $> sudo port install gcc44 $> sudo port select --set gcc mp-gcc44 $> gcc --version gcc (MacPorts gcc44 4.4.7_10) 4.4.7 }}} Download and install the prebuilt package of open-source libraries: {{{ $> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/MacOSX_Lion_Packages.tar.gz $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz |
| Line 20: | Line 58: |
| === Set Your Path === | |
| Line 21: | Line 60: |
| # Dev version: cvs checkout -P dev # Stable version: cvs checkout -P -r stable5 dev |
$> export PATH=/usr/pubsw/packages/autotools/bin:$PATH |
| Line 28: | Line 63: |
| === 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 [[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: |
=== 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 {{{/User/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.) |
| Line 34: | Line 66: |
| 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 [[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 === Set Your Path === {{{ export PATH=/usr/pubsw/packages/autotools/bin:$PATH }}} === 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 make -j4 make install |
$> ./setup_configure $> ./configure --prefix=/User/USER/freesurfer $> make -j4 $> make install |
| Line 72: | Line 72: |
Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu |
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 OS X 10.7, 10.9 (Lion and 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:
Or, you can use the super secret git repo which mirrors the CVS repo:
$> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git
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:
MacPorts (for installing gcc)
XQuartz 2.7.5 (OSX versions 10.9 and lower)
XQuartz 2.7.6 (OSX versions 10.10 and higher)
IMPORTANT: 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"". Next, install Xcode Command Line Tools my typing the following on the command line:
$> xcode-select --install
After Xcode has been installed, we need to install gcc v4.4.7 using MacPorts:
$> sudo port install gcc44 $> sudo port select --set gcc mp-gcc44 $> gcc --version gcc (MacPorts gcc44 4.4.7_10) 4.4.7
Download and install the prebuilt package of open-source libraries:
$> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/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 /User/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 --prefix=/User/USER/freesurfer $> make -j4 $> make install
Done! Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu