I just made a PR to neurodocker to support FreeSufer 7.3.2 https://github.com/ReproNim/neurodocker/pull/469
And used that to build the container `pwighton/freesurfer:7.3.2`. I'm pushing it to dockerhub now. It should be available in an hour or so. It hasn't been tested yet, so if folks use it let us know how it goes!
You'll have to mount your FreeSurfer license file and tell FreeSurfer where it's located, e.g. ``` docker run -it --rm \ -v ~/Downloads/license.txt:/license.txt:ro \ -e FS_LICENSE='/license.txt' \ ... pwighton/freesurfer:7.3.2 \ ... ```
For reference, the container `pwighton/freesurfer:7.3.2` was built using the following command: ``` docker run pwighton/neurodocker:20220822 generate docker \ --base-image ubuntu:xenial \ --pkg-manager apt \ --yes \ --freesurfer \ method=binaries \ version=7.3.2 \ | docker build --no-cache --network host -t pwighton/freesurfer:7.3.2 - ```
-Paul ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fsbuild fsbuild@contbay.com Sent: Saturday, August 20, 2022 9:31 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: william.h.robb@vanderbilt.edu william.h.robb@vanderbilt.edu Subject: Re: [Freesurfer] Docker for Freesurfer 7.3.2
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Hello Hudson,
It should work with an existing CentOS 7, 8 or Ubuntu 18, 20, 22 OS image that you already have running in docker to download and install the freesurfer 7.3.2 .rpm or .deb package. You just need to download the Freesurfer 7.3.2 package that matches your OS into the container from https://freesurfer.net/fswiki/rel7downloads and install it locally, e.g.,
… inside your container use wget or curl from the command line to fetch the package ... $ cd /tmp $ wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/<rpm or deb file matching your OS> … for rpm file (RedHat, CentOS) ... $ sudo yum install ./<rpm file matching your OS> … for deb file (Ubuntu) … $ sudo apt-get install ./<deb file matching your OS> … answer yes to queries if you want to commit to installing what will be added to the system …
When the installation finishes, look to see you have a subdirectory under /usr/local/freesurfer named after the 7.3.2 release, e.g., something like /usr/local/freesurfer/7.3.2. That path should become the setting for the environment variable FREESURFER_HOME.
- R.
On Aug 20, 2022, at 17:05, Robb, William Hudson william.h.robb@vanderbilt.edu wrote:
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Hello,
When is the Freesurfer 7.3.2 docker expected to be released? I see 7.2.0 available here but not 7.3.2 : MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://hub.docker.com/r/freesurfer/freesurfer/tags
Thank you, Hudson Robb _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu