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/
> msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%
> 3DDiZEcZfDkU8Nzjnn41pEiwcA%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.
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
