This is not expected. 

You would need to provide more details (recon-all.log) for anyone to be able to help you. It might be also worth googling the specific error message before hand - it could be that someone else run into this before.

Best,
Chris

On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson <dkp@email.arizona.edu> wrote:
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 <dkp@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.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)
==============
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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
==============



--
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
==============

--
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+unsubscribe@googlegroups.com.
To post to this group, send email to bids-discussion@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/bids-discussion/CAGpV9FLW%2BwK35GD__pJ5VCP0Gd2jguUqym%3Dn38M6qyjss5ekTw%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.