freesurfer bids container fails to find license file

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Dianne Patterson

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Jan 22, 2018, 10:14:17 PM1/22/18
to frees...@nmr.mgh.harvard.edu, bids-di...@googlegroups.com
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



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Chris Gorgolewski

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Jan 22, 2018, 10:19:58 PM1/22/18
to bids-discussion, freesurfer
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

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Dianne Patterson

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Jan 22, 2018, 11:54:48 PM1/22/18
to bids-di...@googlegroups.com, freesurfer
Wonderful...and makes total sense!  Thankyou...it is off and running now.
-Dianne



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Dianne Patterson

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Feb 3, 2018, 10:56:41 PM2/3/18
to bids-di...@googlegroups.com, freesurfer
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

Chris Gorgolewski

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Feb 4, 2018, 10:43:52 AM2/4/18
to bids-discussion, freesurfer
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

Dianne Patterson

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Feb 4, 2018, 12:30:01 PM2/4/18
to bids-di...@googlegroups.com, freesurfer
Dear All, 
Pardon my ignorance.  I am trying freesurfer for the first time, using the BIDS docker container and the standard dataset ds005.
Although I have specified 2 participants to run, freesurfer exits with errors after the first (and does the same if I run the 2nd subject separately).
I am attaching the 3 logs which I take to be most relevant.  I'd be happy to provide other logs if they would be useful for understanding the problem. 
Any insight into why this is happening would be much appreciated.

Thanks,

Dianne

On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski <krzysztof.gorgolewski@gmail.com> wrote:
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 <d...@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




recon-all.error
recon-all-status.log
recon-all.log

Chris Gorgolewski

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Feb 4, 2018, 12:52:34 PM2/4/18
to bids-discussion, freesurfer
This looks like a memory issue to me as indicated bu those two lines:

/opt/freesurfer/bin/reconbatchjobs: line 81:  4014 Killed                  exec $JOB >> $LOG 2>&1
/opt/freesurfer/bin/reconbatchjobs: line 81:  4017 Killed                  exec $JOB >> $LOG 2>&1

You can adjust how much memory of your host machine will be accessible to your docker containers. More details here: https://docs.docker.com/docker-for-mac/#memory

Best,
Chris

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Dianne Patterson

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Feb 4, 2018, 1:52:16 PM2/4/18
to bids-di...@googlegroups.com, freesurfer
Thanks so much! Docker had 2 GB of ram, now it has 10...we'll see if that makes it happy.

-Dianne


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