Freesurfer setup notes

Owned by Paul Macey (admin)
Last updated: Aug 23, 2023
3 min read

  • The license file (“license.txt”) is easy to get, so don’t worry if you don’t have an existing license. Just ask follow the link to fill in the form to request another one if you are setting up on a new system.

Use tar

Chang the permissions of local so it can be read

sudo chmod -R 777 /usr/local

Download the tar.gz file, move it to /usr/local

Open a terminal in /usr/local, unpack

tar -xvzf freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz

Stuff that does not work

  • Use the Ubuntu “DEB installer” download

  • Before installing the freesurfer download, install the dependencies (https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements ) .

    • Note: use apt rather than apt-get

    • It is not unusual for these commands to not work as listed. So, go through these steps from a terminal (“#” is for comments):

...:~$ sudo apt-get -y update # update all installed software # Try this ~$ sudo apt-get -y install git wget tcsh xxd build-essential gfortran # If there are errors, see suggestions in terminal. For example, you might run ~$ sudo apt --fix-broken install # Then repeat install - these are copied from webpage (18 August 2023) ~$ sudo apt-get -y install git wget tcsh xxd build-essential gfortran ~$ sudo apt-get -y install libblas-dev liblapack-dev zlib1g-dev ~$ sudo apt-get -y install libxmu-dev libxmu-headers libxi-dev libxt-dev libx11-dev libglu1-mesa-dev

  • You can try installing with the Software Install tool, and it will report if there are more dependency problems.

  • To find the dependencies, go to a terminal (since the software tool does not report what dependencies are missing).

    • Open a terminal in Downloads and run the command line install:

Look for names of packages not installed, and install those

  • Example:

Look for names of packages not installed, and install those. This is a hunt. In order to install new packages, yuo’ll need to uninstall freesurfer -

Then install what you need

Who knows, yuo might want to run these two

However, we might want to use gdebi because unlike dpkg it resolves dependencies

However, this does nto work. We need the libbrotli1 library. So

https://github.com/google/brotli

From here, we can install the latest brotli, which has that library. However, the package manager does not recognize the updated version. Thus, we are left to abandon the *.deb route.