Diff for "UpdateFreeview" - Free Surfer Wiki

Differences between revisions 2 and 16 (spanning 14 versions)

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.

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

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.
```
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
```

Backup your existing freeview file. This may require sudo access:

mv $FREESURFER_HOME/bin/freeview $FREESURFER_HOME/bin/freeview.backup

Download the latest development version of freeview using the following commands. This may require sudo access:

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

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:
freeview_osx.tar.gz
Untar freeview within your $FREESURFER_HOME (this may require sudo):
```
cd $FREESURFER_HOME
tar -xzvf /path/to/freeview_osx.tar.gz
```

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

-  ⇤ ← Revision 2 as of 2017-04-18 18:26:44 → 
  Size: 1333
  Editor: ZekeKaufman
  Comment:
+   ← Revision 16 as of 2018-11-21 16:16:21 → ⇥
  Size: 2424
  Editor: AndrewHoopes
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-''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 developement version.''
+''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.''
 Line 7:
-. Go into your {{{$FREESURFER_HOME/bin}}} and create a backup of your existing {{{freeview.bin}}} file (this ''may'' require sudo access):
+. '''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.
 Line 10:
-cd $FREESURFER_HOME/bin
cp freeview.bin freeview.bin.BKP
+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
 Line 14:
-. 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:
+. Backup your existing `freeview` file. This may require sudo access:
-Line 21:
+Line 17:
-$FREESURFER_HOME/bin
chmod a+x freeview.bin
+mv $FREESURFER_HOME/bin/freeview $FREESURFER_HOME/bin/freeview.backup
 }}}

 3. Download the latest development version of freeview using the following commands. This may require sudo access:

 {{{
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
 }}}


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

 {{{
freeview
-Line 26:
+Line 35:
+. 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:
 [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/freeview_osx.tar.gz|freeview_osx.tar.gz]]

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

 {{{
cd $FREESURFER_HOME
tar -xzvf /path/to/freeview_osx.tar.gz
 }}}
 
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