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:
On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson <d...@email.arizona.edu>
> 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
> 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
> Any insight into why this is happening would be much appreciated.
> 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.
>> On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson <d...@email.arizona.edu>
>>> 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
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --participant_label 01 02 --license_file
>>> 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?
> Dianne Patterson, Ph.D.
> Research Scientist
> d...@email.arizona.edu <d...@u.arizona.edu>
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> (Just East of Harvill)
> If you don't hear back from me (and you expected to),
> I blame the University's new SPAM filter.
> Please write to my gmail account.
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