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
>>> ==============
>>>
>>> --
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>>> 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%
>> 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
> ==============
>
--
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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