External Email - Use Caution        

Hi All

 

As a frequent user of minctools, I know I’ve had problems in the past if I source minctools before sourcing freesurfer in the same terminal, because freesurfer uses an older version of minctools.

Also, freesurfer uses minc1 format not minc2.

 

Best,

 

Trisanna Sprung-Much

Research Associate

McGill University

MD Anderson Cancer Centre

-- 

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 10, 2021 at 9:54 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mincRead error

 

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Michele Valotti <michele.valotti@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.valotti@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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