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.gorgolewski@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 <dkp@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_TESTING/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

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