Diff for "UpdateFreeview" - Free Surfer Wiki

Differences between revisions 1 and 18 (spanning 17 versions)

This page describes how to update Freeview within a FreeSurfer v6 installation. 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). This step uses the centos6 distribution as an example, but the centos7 tarball can be used as well.
```
mkdir freesurfer.tmp && cd freesurfer.tmp
curl https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos6_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
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:
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 1 as of 2017-04-18 18:23:21 → 
  Size: 791
  Editor: ZekeKaufman
  Comment:
+   ← Revision 18 as of 2019-09-20 14:16:17 → ⇥
  Size: 2300
  Editor: AndrewHoopes
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-This page describes how to update Freeview within a !FreeSurfer v6 installation.
+This page describes how to update Freeview within a !FreeSurfer v6 installation. 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.''
-Line 5:
+Line 7:
-. Go into your {{{$FREESURFER_HOME/bin}}} and create a backup of your existing {{{freeview.bin}}} file (this ''may'' require sudo access):
+. Download and untar the dev freesurfer distribution into a temporary directory (this can be done in any directory). This step uses the centos6 distribution as an example, but the centos7 tarball can be used as well.
-Line 8:
+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-centos6_x86_64-dev.tar.gz -o fsdev.tar.gz
tar -xzvf fsdev.tar.gz
-Line 12:
+Line 15:
-. 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:
+. '''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 19:
+Line 18:
-$FREESURFER_HOME/bin
chmod a+x freeview.bin
+rm -rf ${FREESURFER_HOME}/lib/qt
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
-Line 24:
+Line 38:
+. 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