Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed
minc tools separately on your local machine and do you have any of these
variables set in your default environment?
MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR
It’s possible there’s another install of MNI that’s interfering with the
freesurfer one.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti
<michele.valo...@gmail.com>
Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mincRead error
External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version
on my local machine (where the command runs) and in the cloud instance
On Fri, 5 Feb 2021 at 18:02, Michele Valotti
<michele.valo...@gmail.com<mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local
machine I tried to run it on a server (which should however have the same
FreeSurfer version and setup), but I am getting this error
mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34
UTC 2020 x86_64 GNU/Linux
recon-all -s base_freesurfer exited with ERRORS at Fri Feb 5 17:45:34 UTC 2021
Any idea what the cause of this might be?
Thank you!
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