External Email - Use Caution
Hello Everyone, If you previously downloaded the Ubuntu VM via the link,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - then without any modifications, it should contain both the previous freesurfer 6.0.0 release and the 7.0.0 beta 1 release from April 2020. Please note that latest version 7 release is now 7.1.0 (May 2020) which contains an important update by development that you will want to have if you are using the version 7 release (see copy of email below posted to the list yesterday). Use the following steps to update the 7.0.0-1 release to the 7.1.0 release in the VM. There is also an attached bashrc file to replace the existing one in the home directory for the default user, developer. - R.
- - - - - Update Steps - - - - Download the latest release - currently 7.1.0 - from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-linu...
Let'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
-------- Forwarded Message -------- Subject: [Freesurfer] Release 7.0.0 is being recalled, 7.1.0 is ready for downloadDate: Mon, 11 May 2020 21:58:31 -0400From: Douglas N. Greve <dgreve@mgh.harvard.edu>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Hi All, I regret to inform you that we are recalling 7.0.0 because we found some small issues with the way that conforming step was being performed. The conforming step takes your input volume and converts it to 256x256x256 1mm and converts the type to UCHAR (8 bit). When converting to UCHAR, it has to do some intensity rescaling. The method for doing this was changed in 7.0.0. In most data sets, this results in small changes to the output. However, we just discovered that it can result in large problems in some data sets, so, for 7.1.0, we are reverting back to the pre-7.0.0 method. Going forward, we recommend that people NOT use 7.0.0 and use 7.1.0 instead. We apologize for any inconvenience this has caused.. We hope that not many data sets have been analyzed yet in the 11 days since the release. I'd like to thank our research assistant Devani Cordero for ferreting out this problem.Release notes are here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes7.1.0 can be obtained from here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsPlease let us know if you have any problemsbestdoug