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.
or
dian...@gmail.comUniversity of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
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