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.gorgolewski@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 <dkp@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
dkp@email.arizona.edu

or 

diannepat@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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--

Dianne Patterson, Ph.D.

Research Scientist
dkp@email.arizona.edu

or 

diannepat@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

==============