Maybe you can report back with the version of Debian linux you are using so we could look into it.
You could try downloading and running the Ubuntu VM image we have with freesurfer 6 and 7 beta release installed on it. If you are going to run the VM on a linux machine, then you should still be able to follow the instructions listed for setting up the VM on either the Mac or Windows after you install VirtualBox on your linux machine. The links to the VirtualBox setup instructions for MacOS and Windows are here,
Once you get the Ubuntu VM running and login as userid developer, you can update the beta 7 release to the latest 7.1.0 release with the instructions below.
You can email me directly if you run into something.
- R.
- - - - - Updating Ubuntu FS 7 beta release to the current 7.1.0 release - - - -
Log into the Ubuntu VM as aid developer.
Download the latest release - currently 7.1.0 - from
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-linux-centos7_x86_64-7.1.0.tar.gzLet's assume after the download the archive file is located in your downloads folder under the path,
~/Downloads/freesurfer-linux-centos7_x86_64-7.1.0..tar.gz
Locate your previous version 7 release under the path /usr/local/freesurfer
$ ls /usr/local/freesurfer
6.0.0-1 7..0.0-1
Remove the previous version 7 release, here 7.0.0-1,
$ cd /usr/local/freesurfer
$ sudo rm -rf 7.0.0-1
Expand the archive for the new release from your downloads folder,
$ sudo tar zxpf ~/Downloads/freesurfer-linux-centos7_x86_64-7.1.0..tar.gz
Now move the newly created ./freesurfer subdirectory from the archive to be the name of the new release,
$ sudo mv freesurfer 7.1.0-1
Check to see files are there,
$ ls 7.1.0-1
<output deleted>
Finally, replace your existing $HOME/.bashrc file with the attached bashrc file which will
allow you to run either the 6.0.0 or 7.1.0 release. NOTE - if you have made changes to
your $HOME/..bashrc file since you started using the VM, then you may want to merge your
current $HOME/.bashrc with the contents of the attached bashrc in order not to lose your
changes. You could also diff the 2 files and add manually edit in the changes from the
attached bashrc.
With the new bashrc in your downloads folder as ~/Downloads/bashrc, then to diff the files,
$ diff ~/Downloads/bashrc $HOME/.bashrc
To simply replace the old bashrc in its entirety,
$ cp -p -f ~/Downloads/bashrc $HOME/.bashrc
Once your new $HOME/.bashrc file is in place (which should use use the 7.1.0-1 release
by default), then start a new terminal window. You should see the following output:
-------- freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/7.1.0-1
FSFAST_HOME /usr/local/freesurfer/7.1.0-1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/7.1.0-1/subjects
TUTORIAL_DATA /home/developer/tutorial_data
MNI_DIR /usr/local/freesurfer/7.1.0-1/mni
WARNING: /usr/local/freesurfer/7.1.0-1/fsl_507/bin does not exist.
FSL_DIR /usr/local/freesurfer/7.1.0-1/fsl_507
On May 19, 2020, at 12:14, Gian Marco Duma <gianmarco.duma@phd.unipd.it> wrote:
External Email - Use Caution
Hi everyone, I have a problem with freeview. My university created for me a virtual machine in a small analysis cluster. Unfortunately, they installed Debian 4.19.98. I read that freeview has some problems with Debian, and in fact I am not able to open it. Unfortunately I need to visualize the data because we are conducting an anatomical study with patients with lesions. All the processes I ran until now, like automatic segmentation and surface generation like recon all, worked perfectly, but I need to visualize the data. Do you have suggestions to solve this problem?
Thanks
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