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_
> 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
>
> On Mon, Jan 22, 2018 at 9:54 PM, Dianne Patterson <d...@email.arizona.edu>
> wrote:
>
>> Wonderful...and makes total sense!  Thankyou...it is off and running now.
>> -Dianne
>>
>>
>> On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski <
>> krzysztof.gorgolew...@gmail.com> wrote:
>>
>>> Hi Dianne,
>>>
>>> You need to "mount" the using -v the same way input and output
>>> directories are mounted. For example:
>>>
>>> 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 --license_file /license.txt
>>>
>>> Best,
>>> Chris
>>>
>>> On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson <d...@email.arizona.edu
>>> > wrote:
>>>
>>>> Dear All,
>>>>
>>>> After trying the example bids app (which worked fine), I am trying the
>>>> freesurfer bids app. I have built the docker container on my mac and I have
>>>> the ds005 data directory here and the license.txt which I requested from
>>>> freesurfer.
>>>> I asked for a linux license (assuming the container contains linux and
>>>> that was the relevant fact).
>>>>
>>>> dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
>>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
>>>> /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>>> /bids_dataset /outputs participant --license_file "license.txt"
>>>> 1: You should define 'SliceTiming' for this file. If you don't provide
>>>> this information slice time correction will not be possible. (code: 13 -
>>>> SLICE_TIMING_NOT_DEFINED)
>>>> /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
>>>> /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
>>>> /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
>>>> /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
>>>> /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
>>>> /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
>>>> /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
>>>> /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
>>>> /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
>>>> /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
>>>> ... and 38 more files having this issue (Use --verbose to see them all).
>>>>
>>>>         Summary:                 Available Tasks:          Available
>>>> Modalities:
>>>>         133 Files, 1.77GB        mixed-gambles task        T1w
>>>>         16 - Subjects                                      inplaneT2
>>>>         1 - Session                                        bold
>>>>
>>>>
>>>> Traceback (most recent call last):
>>>>   File "/run.py", line 165, in <module>
>>>>     raise Exception("Provided license file does not exist")
>>>> *Exception: Provided license file does not exist*
>>>> ===========
>>>> If I provide the full path to the license file, it still fails:
>>>>
>>>> docker run -ti --rm -v 
>>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>>> /bids_dataset /outputs participant --license_file
>>>> "/Volumes/Main/Working/BIDS_TESTING/license.txt"
>>>>
>>>> Suggestions?  How do I tell freesurfer where the license file is?
>>>>
>>>> Thanks so much,
>>>>
>>>> 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/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8
>>>> Nzjnn41pEiwcA%40mail.gmail.com
>>>> <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8Nzjnn41pEiwcA%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/ms
>>> gid/bids-discussion/CAAQzouN_u48OSsJ-R1wR8QaTe-QL94zuR%2BjLx
>>> oM4WexfFi-QKA%40mail.gmail.com
>>> <https://groups.google.com/d/msgid/bids-discussion/CAAQzouN_u48OSsJ-R1wR8QaTe-QL94zuR%2BjLxoM4WexfFi-QKA%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
>> <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
>> ==============
>>
>
>
>
> --
> 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/
> msgid/bids-discussion/CAGpV9FLW%2BwK35GD__pJ5VCP0Gd2jguUqym%
> 3Dn38M6qyjss5ekTw%40mail.gmail.com
> <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FLW%2BwK35GD__pJ5VCP0Gd2jguUqym%3Dn38M6qyjss5ekTw%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
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