Thanks so much! Docker had 2 GB of ram, now it has 10...we'll see if that makes it happy.
-Dianne On Sun, Feb 4, 2018 at 10:52 AM, Chris Gorgolewski < krzysztof.gorgolew...@gmail.com> wrote: > 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) >> ============== >> 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. >> ============== >> Antipiphany: That moment when you realize how little you actually know >> ============== >> >> -- >> You received this message because you are subscribed to the Google Groups >> "bids-discussion" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to bids-discussion+unsubscr...@googlegroups.com. >> To post to this group, send email to bids-discuss...@googlegroups.com. >> To view this discussion on the web visit https://groups.google.com/d/ms >> gid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L >> 0iEgFiUQQdqvw%40mail.gmail.com >> <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L0iEgFiUQQdqvw%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups > "bids-discussion" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to bids-discussion+unsubscr...@googlegroups.com. > To post to this group, send email to bids-discuss...@googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/ > msgid/bids-discussion/CAAQzouPqR4nafHdo%3DJVjD4%2Bg11%3DhMcse_ttsw-xfBo_ > 0SznMAw%40mail.gmail.com > <https://groups.google.com/d/msgid/bids-discussion/CAAQzouPqR4nafHdo%3DJVjD4%2Bg11%3DhMcse_ttsw-xfBo_0SznMAw%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > > For more options, visit https://groups.google.com/d/optout. > -- 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 (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. ============== Antipiphany: That moment when you realize how little you actually know ==============
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