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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. '''NOTE:''' if you are using a version of freeview released before Nov 2018, you must run the following commands (with `FREESURFER_HOME` properly set) to update the appropriate Qt and VTK libraries . Otherwise, you can skip to step 2. | 1. Download and untar the dev freesurfer distribution into a temporary directory (this can be done in any directory). |
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| rm -rf ${FREESURFER_HOME}/lib/qt ${FREESURFER_HOME}/bin/freeview.bin wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/data/fvlib/freeview-lib-update.tar.gz | tar xvz -C ${FREESURFER_HOME}/lib |
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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| 2. Create a backup of your existing `freeview` file (this ''may'' require sudo access): | 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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| cp $FREESURFER_HOME/bin/freeview $FREESURFER_HOME/bin/freeview.backup | 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/ |
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| 3. Download the latest development version of freeview using the following commands. This may require sudo access: | 3. Remove the temporary directory: |
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| wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/freeview -P ${FREESURFER_HOME}/bin chmod +x ${FREESURFER_HOME}/bin/freeview |
cd .. && rm -rf freesurfer.tmp |
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| 4. You should now have the new freeview application which is opened by typing {{{freeview}}} on the command line (after sourcing Freesurfer): | 4. You should now have the new application, which can opened by typing `freeview` on the command line: |
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| 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]] |
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| tar -xzvf /path/to/freeview_osx.tar.gz | tar -xzvf /path/to/freesurfer-darwin-macOS_HighSierra-dev-freeview.tar.gz |
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| 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
- 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
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/- Remove the temporary directory:
cd .. && rm -rf freesurfer.tmp
You should now have the new application, which can opened by typing freeview on the command line:
freeview
Mac
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
Download the dev, standalone freeview tarball from here
Untar freeview within your $FREESURFER_HOME (this may require sudo):
cd $FREESURFER_HOME tar -xzvf /path/to/freesurfer-darwin-macOS_HighSierra-dev-freeview.tar.gz
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