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Oops, forget about the log file. 
Here it is


------------------ Original ------------------
From: "xuan" <pearl940311@foxmail.com>;
Date: Wed, Dec 15, 2021 08:28 PM
To: "freesurfer"<freesurfer@nmr.mgh.harvard.edu>;
Subject: nu_correct error

Dear FreeSurfer Experts,

I am attempting to recon-all for my one subject for testing on my lab server. However, I get following error:

ncopen: filename "./tmp.mri_nu_correct.mni.13492/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.13492/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.13492/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.13492/nu1.mnc...

And here is the relevant information:
(1)FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
(2)Platform: Linux node-1-3 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
(3)log file: please see attached file.

Thanks for the help!

Best,
Xuan


Xuan Bu, Ph.D.

State Key Laboratory of Cognitive Neuroscience & Learning
Beijing Normal University
Email: pearl904311@foxmail.com
Webpage: http://helab.bnu.edu.cn/xuanbu/