Differences between revisions 13 and 26 (spanning 13 versions)
⇤ ← Revision 13 as of 2018-09-27 12:11:03 →
Size: 2378
Editor: AndrewHoopes
Comment:
← Revision 26 as of 2021-05-19 14:42:33 → ⇥
Size: 2295
Editor: AndrewHoopes
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
This page describes how to update Freeview within a !FreeSurfer v6 installation. On Linux this involves updating a single file in your {{{FREESURFER_HOME/bin}}} directory. On Mac it involves replacing the Freeview.app folder in your {{{FREESURFER_HOME}}} directory. A backup should always be made of the file (or directory) before it is replaced. This page describes how to update Freeview within a !FreeSurfer installation of version 6 or greater. A backup should be made of your freeview binary (or directory) before it is replaced.
Line 7: Line 7:
WARNING: the freeview development install on linux is currently broken due to upgrades to the Qt and VTK libraries. This should be resolved soon.

 1. Go into your {{{$FREESURFER_HOME/bin}}} and create a backup of your existing {{{freeview.bin}}} file (this ''may'' require sudo access):		  1. Download and untar the dev freesurfer distribution into a temporary directory (this can be done in any directory).
Line 12: Line 10:
cd $FREESURFER_HOME/bin
cp freeview.bin freeview.bin.BKP		 mkdir freesurfer.tmp && cd freesurfer.tmp
curl https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz -o fsdev.tar.gz
tar -xzvf fsdev.tar.gz
Line 16: Line 15:
 1. Download the latest "development version" of Freeview using the following link. Again, overwriting the original {{{freeview.bin}}} file may require sudo access:

 [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/freeview.bin|freeview.bin]]

 1. Make sure the new {{{freeview.bin}}} file is made executable. This is acheived via the following command:		  2. '''IMPORTANT''': make sure that `FREESURFER_HOME` is properly set to the '''original''' freesurfer install you'd like to update, and copy the new freeview binary and qt libraries over. This may require sudo access:
Line 23: Line 18:
cd $FREESURFER_HOME/bin
chmod a+x freeview.bin		 rm -rf ${FREESURFER_HOME}/lib/qt ${FREESURFER_HOME}/lib/vtk
cp -r freesurfer/lib/qt ${FREESURFER_HOME}/lib/qt
cp -r freesurfer/lib/vtk ${FREESURFER_HOME}/lib/vtk
cp freesurfer/bin/freeview freesurfer/bin/qt.conf ${FREESURFER_HOME}/bin/
Line 27: Line 24:
 1. You should now have the new freeview application which is opened by typing {{{freeview}}} on the command line (after sourcing Freesurfer):  3. Remove the temporary directory:

 {{{
cd .. && rm -rf freesurfer.tmp
 }}}


 4. You should now have the new application, which can opened by typing `freeview` on the command line:
Line 42: Line 46:
 2. Download the dev, standalone freeview tarball from here:
 [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/freeview_osx.tar.gz|freeview_osx.tar.gz]]		  2. Download the dev, standalone freeview tarball from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/freesurfer-darwin-macOS-dev-freeview.tar.gz|here]]
Line 49: Line 52:
tar -xzvf /path/to/freeview_osx.tar.gz tar -xzvf /path/to/freesurfer-darwin-macOS-dev-freeview.tar.gz
Line 52: Line 55:
4. If you are replacing freeview in a stable freesurfer release, then you must also remove the line "`source $FREESURFER_HOME/sources.csh`" from the `$FREESURFER_HOME/bin/freeview` script  4. '''IMPORTANT''': If you are replacing freeview in a freesurfer release LESS than 7.0, then you must also remove the line "`source $FREESURFER_HOME/sources.csh`" from the `$FREESURFER_HOME/bin/freeview` script

This page describes how to update Freeview within a FreeSurfer installation of version 6 or greater. A backup should be made of your freeview binary (or directory) before it is replaced.

Please note the development versions of Freeview will contain the most up to date features but lacks the rigorous testing done before a major release. Therefore, it is imperative that you back up your existing version before replacing it with the development version.

Linux

  1. Download and untar the dev freesurfer distribution into a temporary directory (this can be done in any directory). 
    mkdir freesurfer.tmp && cd freesurfer.tmp
curl https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz -o fsdev.tar.gz
tar -xzvf fsdev.tar.gz

  2. IMPORTANT: make sure that FREESURFER_HOME is properly set to the original freesurfer install you'd like to update, and copy the new freeview binary and qt libraries over. This may require sudo access: 

    rm -rf ${FREESURFER_HOME}/lib/qt ${FREESURFER_HOME}/lib/vtk
cp -r freesurfer/lib/qt ${FREESURFER_HOME}/lib/qt
cp -r freesurfer/lib/vtk ${FREESURFER_HOME}/lib/vtk
cp freesurfer/bin/freeview freesurfer/bin/qt.conf ${FREESURFER_HOME}/bin/
  3. Remove the temporary directory: 
    cd .. && rm -rf freesurfer.tmp

  4. You should now have the new application, which can opened by typing freeview on the command line: 

    freeview

Mac

  1. Go into your $FREESURFER_HOME and create a backup of your existing freeview app (this may require sudo access): 

    cd $FREESURFER_HOME
cp Freeview.app Freeview-backup.app

  2. Download the dev, standalone freeview tarball from here

  3. Untar freeview within your $FREESURFER_HOME (this may require sudo): 

    cd $FREESURFER_HOME
tar -xzvf /path/to/freesurfer-darwin-macOS-dev-freeview.tar.gz

  4. IMPORTANT: If you are replacing freeview in a freesurfer release LESS than 7.0, then you must also remove the line "source $FREESURFER_HOME/sources.csh" from the $FREESURFER_HOME/bin/freeview script

UpdateFreeview (last edited 2025-11-06 17:56:38 by buildqa)