Differences between revisions 13 and 17 (spanning 4 versions)
⇤ ← Revision 13 as of 2013-09-23 14:10:05 →
Size: 2830
Editor: ZekeKaufman
Comment:
← Revision 17 as of 2013-09-25 12:22:15 → ⇥
Size: 2907
Editor: ZekeKaufman
Comment:
Deletions are marked like this. Additions are marked like this.
Line 22: Line 22:
Or, you can get readonly CVS access to the source code by using following the directions [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS|on this page]]:
Line 23: Line 27:
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:
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:
Line 27: Line 37:
tar -C /usr/pubsw/packages -xzvf DownLoadedFileName.tar.gz tar -C /usr/pubsw/packages -xzvf DownloadedFileName.tar.gz
Line 30: Line 40:
'''''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		 '''''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"')
Line 39: Line 47:
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.)
Line 46: Line 54:
      --prefix=/Users/USER/freesurfer       --prefix=/Users/USER/freesurfer \
      --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

Or, you can get readonly CVS access to the source code by using following the directions on this page:

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