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 mreuter@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 miracooloz@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

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