subject:"\[Freesurfer\] \[bids\-discussion\] freesurfer bids container fails to find license file"

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

2018-02-04 Thread Dianne Patterson

Thanks so much! Docker had 2 GB of ram, now it has 10...we'll see if that
makes it happy.

-Dianne

On Sun, Feb 4, 2018 at 10:52 AM, Chris Gorgolewski <
krzysztof.gorgolew...@gmail.com> wrote:

> 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
>
> On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson 
> wrote:
>
>> 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.gorgolew...@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 
>>> 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_TES
 TING/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


>>
>>
>> --
>> Dianne Patterson, Ph.D.
>> Research Scientist
>> d...@email.arizona.edu 
>> or
>> dianne...@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+unsubscr...@googlegroups.com.
>> To post to this group, send email to bids-discuss...@googlegroups.com.
>> To view this discussion on the web visit https://groups.google.com/d/ms
>> gid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L
>> 0iEgFiUQQdqvw%40mail.gmail.com
>> 
>> .
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
> --
> 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+unsubscr...@googlegroups.com.
> To post to this group, send email to bids-discuss...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/
> msgid/bids-discussion/CAAQzouPqR4nafHdo%3DJVjD4%2Bg11%3DhMcse_ttsw-xfBo_
> 0SznMAw%40mail.gmail.com
> 
> .
>
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Dianne Patterson, Ph.D.
Research Scientist
d...@email.arizona.edu 
or
dianne...@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.

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

2018-02-04 Thread Chris Gorgolewski

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

On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson 
wrote:

> 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.gorgolew...@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 
>> 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_TES
>>> TING/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
>>>
>>>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> d...@email.arizona.edu 
> or
> dianne...@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+unsubscr...@googlegroups.com.
> To post to this group, send email to bids-discuss...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/ms
> gid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L
> 0iEgFiUQQdqvw%40mail.gmail.com
> 
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
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Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

2018-02-04 Thread Chris Gorgolewski

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 
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 
> 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.gorgolew...@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 >> > 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, 1.77GBmixed-gambles taskT1w
 16 - Subjects  inplaneT2
 1 - Sessionbold

 Traceback (most recent call last):
   File "/run.py", line 165, in 
 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
 d...@email.arizona.edu 
 or
 dianne...@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.

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

2018-02-03 Thread Dianne Patterson

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 
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.gorgolew...@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 
>> 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, 1.77GBmixed-gambles taskT1w
>>> 16 - Subjects  inplaneT2
>>> 1 - Sessionbold
>>>
>>>
>>> Traceback (most recent call last):
>>>   File "/run.py", line 165, in 
>>> 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
>>> d...@email.arizona.edu 
>>> or
>>> dianne...@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+unsubscr...@googlegroups.com.
>>> To post to this group, send email to

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

2018-01-22 Thread Dianne Patterson

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.gorgolew...@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 
> 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, 1.77GBmixed-gambles taskT1w
>> 16 - Subjects  inplaneT2
>> 1 - Sessionbold
>>
>>
>> Traceback (most recent call last):
>>   File "/run.py", line 165, in 
>> 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
>> d...@email.arizona.edu 
>> or
>> dianne...@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+unsubscr...@googlegroups.com.
>> To post to this group, send email to bids-discuss...@googlegroups.com.
>> To view this discussion on the web visit https://groups.google.com/d/ms
>> gid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8
>> Nzjnn41pEiwcA%40mail.gmail.com
>> 
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
>
> --
> 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+unsubscr...@googlegroups.com.
> To post to this group, send email to bids-discuss...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/
> msgid/bids-discussion/CAAQzouN_u48OSsJ-R1wR8QaTe-
> QL94zuR%2BjLxoM4WexfFi-QKA%40mail.gmail.com

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

2018-01-22 Thread Chris Gorgolewski

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 
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, 1.77GBmixed-gambles taskT1w
> 16 - Subjects  inplaneT2
> 1 - Sessionbold
>
>
> Traceback (most recent call last):
>   File "/run.py", line 165, in 
> 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
> d...@email.arizona.edu 
> or
> dianne...@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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> msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%
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> 
> .
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>
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Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

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