External Email - Use Caution
Hi Andrew,
on my machine those variables are all empty but in the container they return in the container
echo $MNI_DIR returns:
echo $MINC_BIN_DIR returns: /usr/local/freesurfer/mni/bin echo $MINC_LIB_DIR returns: /usr/local/freesurfer/mni/lib
I'll try and get the mri_nu_correct.mni.log file
On Wed, 10 Feb 2021 at 14:54, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
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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