Hello Martin, I tried your first suggestion (removing the flags) and I got the same errors. Yes, I do have enough space on the disk and nu1.mnc file does exist. Do you think my script is the problem? I have attached the new recon log file and my script. Thanks.
Best, Paul On Thu, Nov 9, 2017 at 11:13 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi Paul, > > you can try to re-run from scratch (ensure there is enough space on the > disk) and if you can replicate the problem start dropping some of the flags > (like the parallel and the bigventricles etc, to find out if this is caused > by one of the flags.) > > Anyway it looks more like an IO problem > ncopen: filename "./tmp.mri_nu_correct.mni.53099/nu1.mnc": Not a netCDF > file > miopen: MINC package entry point > Error opening ./tmp.mri_nu_correct.mni.53099/nu1.mnc > mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni. > 53099/nu1.mnc > > is that file even there? > > Best, Martin > > > > On 8. Nov 2017, at 19:56, miracle ozzoude <miracoo...@gmail.com> wrote: > > > > Hello FreeSurfer, > > > > While running base step of the longitudinal pipeline, i got the > following error (please see the rec-all.log file for more details). How do > i solve this problem? Thank you > > > > Best, > > Paul > > <recon-all.log>_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
recon-all.error
Description: Binary data
recon-all.log
Description: Binary data
FreeSurferLongitudinal.sh
Description: Bourne shell script
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