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
>> ==============
>>
>> --
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>>
>
> --
> You received this message because you are subscribed to the Google Groups
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> 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/CAAQzouN_u48OSsJ-R1wR8QaTe-
> QL94zuR%2BjLxoM4WexfFi-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
(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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