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