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Hi,

Here's what I've learned from my attempts (eventually successful), to run freesurfer in docker on a mac:

There are three tricks to running the freesurfer *docker* container.

1) You must request a license.txt file from the freesurfer website: https://surfer.nmr.mgh.harvard.edu/fswiki/License

2) You must bind mount the license file on the outside to license.txt on the inside of the container (this is just like binding the input small_ds and outputs directories), e.g.:

docker run -ti --rm -v

/Volumes/Main/Working/BIDS_TESTING/license.txt:/license.txt:ro -v /Volumes/Main/Working/BIDS_TESTING/small_ds:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file /license.txt

3) On the mac, Docker runs in a minimal virtual machine. By default, this machine is allowed to access 2 GB of RAM. recon-all requires more RAM (~4 GB or more) https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements. See instructions here for increasing the RAM on Docker for Mac: https://docs.docker.com/docker-for-mac/#advanced

On Fri, Jul 20, 2018 at 1:13 AM Carolina Bonivento < boniventocarolina@gmail.com> wrote:

    External Email - Use Caution

Apologize, I forgot to attach the file with the license. Here it is.

Best regards,

Carolina

Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento < boniventocarolina@gmail.com> ha scritto:

Dear Sir/Madame, I recently subscribed the FS license (attached) but when I tried to run the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received the following error message:

*ERROR: Invalid FreeSurfer license key found in license file /root/freesurfer/license.txt*

Following some instruction that I got previously, I replaced the .license with the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) but I still get the same error message.

Note that I’m running FreeSurfer through a Docker container running Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High Sierra (of course, Docker and the freesurfer folder are on the same machine). When I filled the license request form I’ve selected Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker container. Is it possible that the issue is due to this? In that case, can I ask for a second license?

Thank you in advance for your attention.

Looking forward to hearing from you, I’m sending you my best regards,

Carolina

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