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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.
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 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).
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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
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 1. Download the latest "development version" of Freeview using the following link. Again, overwriting the origin {{{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:
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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/
 }}}

 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
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 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. Select the tar archive from which you would like to get a copy of the Freeview application bundle. For the latest development builds, these packages would be: freesurfer-macOS-darwin_x86_64-dev.tar.gz for Intel Macs (darwin_x86_64); freesurfer-macOS-darwin_arm64-dev.tar.gz for arm64 Macs with the M1, M2, M3, M4, M5 processors (darwin_arm64). If you are inside the Martinos Center on a machine that mounts /space/freesurfer, you can copy the above files from the in-house path /space/freesurfer/build/pub-releases/dev

 3. Otherwise, for Macs with M-series arm64 processors download [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.tar.gz|freesurfer-macOS-darwin_arm64-dev.tar.gz]]. For older Macs with Intel processors download [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_x86_64-dev.tar.gz|freesurfer-macOS-darwin_x86_64-dev.tar.gz]]

 4. Extract the freeview application bundle from the downloaded archive when you are cd'd to be under {{{$FREESURFER_HOME}}} (this ''may'' require prefacing the tar command with sudo):

 {{{
cd $FREESURFER_HOME
tar -zxpf <path to>/freesurfer-macOS-darwin_arm64-dev.tar.gz Freeview.app
OR
tar -zxpf <path to>/freesurfer-macOS-darwin_x86_64-dev.tar.gz Freeview.app
 }}}
 
 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. Select the tar archive from which you would like to get a copy of the Freeview application bundle. For the latest development builds, these packages would be: freesurfer-macOS-darwin_x86_64-dev.tar.gz for Intel Macs (darwin_x86_64); freesurfer-macOS-darwin_arm64-dev.tar.gz for arm64 Macs with the M1, M2, M3, M4, M5 processors (darwin_arm64). If you are inside the Martinos Center on a machine that mounts /space/freesurfer, you can copy the above files from the in-house path /space/freesurfer/build/pub-releases/dev

  3. Otherwise, for Macs with M-series arm64 processors download freesurfer-macOS-darwin_arm64-dev.tar.gz. For older Macs with Intel processors download freesurfer-macOS-darwin_x86_64-dev.tar.gz

  4. Extract the freeview application bundle from the downloaded archive when you are cd'd to be under $FREESURFER_HOME (this may require prefacing the tar command with sudo): 

    cd $FREESURFER_HOME
tar -zxpf <path to>/freesurfer-macOS-darwin_arm64-dev.tar.gz Freeview.app
OR
tar -zxpf <path to>/freesurfer-macOS-darwin_x86_64-dev.tar.gz Freeview.app

  5. 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)