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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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: 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 ==============
-- 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/ms gid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8 Nzjnn41pEiwcA%40mail.gmail.com https://groups.google.com/d/msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8Nzjnn41pEiwcA%40mail.gmail.com?utm_medium=email&utm_source=footer . For more options, visit https://groups.google.com/d/optout.
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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: 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 ==============
-- 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/ms gid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8 Nzjnn41pEiwcA%40mail.gmail.com https://groups.google.com/d/msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8Nzjnn41pEiwcA%40mail.gmail.com?utm_medium=email&utm_source=footer . For more options, visit https://groups.google.com/d/optout.
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-- 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 (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 ==============
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: 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 ==============
-- 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/ms gid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8 Nzjnn41pEiwcA%40mail.gmail.com https://groups.google.com/d/msgid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8Nzjnn41pEiwcA%40mail.gmail.com?utm_medium=email&utm_source=footer . For more options, visit https://groups.google.com/d/optout.
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-- 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 ==============
-- 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 ==============
-- 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 https://groups.google.com/d/msgid/bids-discussion/CAGpV9FLW%2BwK35GD__pJ5VCP0Gd2jguUqym%3Dn38M6qyjss5ekTw%40mail.gmail.com?utm_medium=email&utm_source=footer .
For more options, visit https://groups.google.com/d/optout.
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 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_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
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 dkp@email.arizona.edu 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.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 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_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 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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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.gorgolewski@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 dkp@email.arizona.edu 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.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 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_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 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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freesurfer@nmr.mgh.harvard.edu
-
Chris Gorgolewski -
Dianne Patterson