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: AvailableModalities: 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 dkp@u.arizona.edu or diannepat@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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