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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Martin Reuter <mreuter@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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