Hi Michele,

Looks like the base error here is:

ncopen: filename "./tmp.mri_nu_correct.mni.6973/nu1.mnc": Not a netCDF file

My immediate guess is this is a version incompatibility. You mentioned that you reinstalled minc tools? How so and with what version? Also, what was the previous nu_correct error you were getting?

best,

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Michele Valotti <michele.valotti@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, January 4, 2021 at 10:49 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mincRead error in recon-all

        External Email - Use Caution        

Dear Freesurfer Team,

I am trying to run recon-all on a test scan, but I am getting this error:

Error opening ./tmp.mri_nu_correct.mni.6973/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.6973/nu1.mnc

(logs attached)

I just reinstalled minc tools due to a nu_correct error I was getting, not sure if this could be a problem. I read on the mailing list that it could be a permission error but trying the suggested solutions did not solve the problem

running    ls -l tmp.mri_nu_correct.mni.3787/nu1.mnc

returns   -rw-rw-r-- 1 michele michele 22990022 Jan  4 15:01 tmp.mri_nu_correct.mni.3787/nu1.mnc

Any help is greatly appreciated

Thank you

Michele