This looks like a memory issue to me as indicated bu those two lines:

/opt/freesurfer/bin/reconbatchjobs: line 81:  4014 Killed
exec $JOB >> $LOG 2>&1
/opt/freesurfer/bin/reconbatchjobs: line 81:  4017 Killed
exec $JOB >> $LOG 2>&1

You can adjust how much memory of your host machine will be accessible to
your docker containers. More details here:
https://docs.docker.com/docker-for-mac/#memory

Best,
Chris

On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson <d...@email.arizona.edu>
wrote:

> Dear All,
> Pardon my ignorance.  I am trying freesurfer for the first time, using the
> BIDS docker container and the standard dataset ds005.
> Although I have specified 2 participants to run, freesurfer exits with
> errors after the first (and does the same if I run the 2nd subject
> separately).
> I am attaching the 3 logs which I take to be most relevant.  I'd be happy
> to provide other logs if they would be useful for understanding the
> problem.
> Any insight into why this is happening would be much appreciated.
>
> Thanks,
>
> Dianne
>
> On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski <
> krzysztof.gorgolew...@gmail.com> wrote:
>
>> This is not expected.
>>
>> You would need to provide more details (recon-all.log) for anyone to be
>> able to help you. It might be also worth googling the specific error
>> message before hand - it could be that someone else run into this before.
>>
>> Best,
>> Chris
>>
>> On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson <d...@email.arizona.edu>
>> wrote:
>>
>>> Since I'm following the example on the github page, using the ds005
>>> dataset, now with the correct license binding, I am surprised to see
>>> freesurfer exiting with errors (but I don't know much about freesurfer):
>>>
>>> I run this:
>>>
>>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_TES
>>> TING/license.txt:/license.txt:ro -v 
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --participant_label 01 02 --license_file
>>> /license.txt
>>>
>>> A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
>>> 03:27:11 UTC 2018
>>> And then sub-02 does not run
>>>
>>> Is this what I should expect?
>>>
>>> Thanks,
>>>
>>> Dianne
>>>
>>>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> d...@email.arizona.edu <d...@u.arizona.edu>
> or
> dianne...@gmail.com
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371&entry=gmail&source=g>
> (Just East of Harvill)
> ==============
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> Please write to my gmail account.
> ==============
> Antipiphany: That moment when you realize how little you actually know
> ==============
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