Hi Sneha,
Yes, mixing versions could also produce problems. 5.1 works in native
spaces all the way trough to the long runs, while 5.3 works in the base
space for the long runs. Don't mix versions.
Best, Martin
On 04/01/2016 12:38 PM, Sneha Pandya wrote:
Hi Martin,
Yes, I indeed checked the log file and saw so many errors, and was
therefore very surprised as to how did it run through the pipeline
without any error message. Thank you so much. I shall look at the
specs for the disk space and notify if something unusual occurs. But
its strange that we ran few more after similar failures and they seem
to have run fine without these issues.
Also I wanted to point out that we are running these cases from two
different servers pointing to same mount directory where all the
processing has been running. One version of FS is 5.1 as you notified
and other is 5.3. It could have been possible that we ran
cross-sectional and base from either of these servers and ran
longitudinal from other. Could that also be part of the reason for its
failure because of IO? Do you suggest we should stick to only one
server for cross-section to longitudinal run for different time points
of same subjects?
Thanks,
Sneha
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter
<mreu...@nmr.mgh.harvard.edu>
*Sent:* Friday, April 1, 2016 12:18 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Longitudinal recon-all fail
Hi Sneha,
looks like an IO problem, maybe the disk is full or the mount was broken?
Strange that is reports finished without error, when in fact there are
many errors (if you scroll up you can see many 'file not found'
messages). Anyway. This is 5.1 and very old. I would recommend to
check the IO disk space thing above and rerun these cases.
Best, Martin
On 04/01/2016 11:36 AM, Sneha Pandya wrote:
Dear experts,
We are running longitudinal pipeline for bunch of our MS
subjects. Longitudinal recon-all failed to create volumes and
surfaces for few of our subjects. We ran cross-sectional and did all
the edits on them and after that ran base script without any issues
or errors. When we run longitudinal on them it runs recon-all fine
without exiting with errors. However it did not create important
surfaces and volumes. Please find attached log file for one of the
longitudinal timepoints for details.
Not sure why did they fail only for few of them as we have ran 100s
of them with no issue earlier. Any advice will be of great help!
Thanks,
Sneha
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web :http://reuter.mit.edu
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Freesurfer mailing list
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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