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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of fsbuild
<fsbu...@contbay.com>
Sent: Saturday, August 20, 2022 9:31 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: william.h.r...@vanderbilt.edu <william.h.r...@vanderbilt.edu>
Subject: Re: [Freesurfer] Docker for Freesurfer 7.3.2
External Email - Use Caution
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.r...@vanderbilt.edu>
wrote:
External Email - Use Caution
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
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Freesurfer@nmr.mgh.harvard.edu
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