It may be the version of minc you are using. On our system, we use version 1.5, but it seems to work with 2.2. I don't have access to 2.3. Can you try this

mri_convert orig.mgz orig.nii
nii2mnc orig.nii junk.mnc
mri_convert junc.mnc junk.mgh

I'm thinking that the last command will fail

On 2/7/17 6:27 PM, Muhammad Khan wrote:

Thanks for getting back to me.

I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this is the output:

-rw-rw-r-- 1 root 1590 31M Feb  7 10:14 ./tmp.mri_nu_correct.mni.30405/nu1.mnc

I do have multiple disks mounted on the server, but they all have more than enough space. The directory of the freesurfer folder has over 1.5TB. Are any temporary folders created in a different location other than the freesurfer directory?

Thanks!

On Tue, Feb 7, 2017 at 4:21 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

not sure what is going wrong here. For some reason mri_convert does not think that the mnc file is a minc file. Can you verify that you did not run out of space on that disk? Can you send the result of

ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc

On 2/7/17 2:59 PM, Muhammad Khan wrote:

Hi FreeSurfer Developers,

I have been trying the 'recon-all -all -s TEST01' command, however I run into the following error:

mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz --like orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc...
Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TEST01 exited with ERRORS at Tue Feb  7 10:14:31 PST 2017
For more details, see the log file /mnt/data/freesurfer/subjects/TEST01/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I tried looking in the email-archives, although people had the same error, I wan unable to find a fix for it. My linux server is running on CentOS 6.8 and I am using the latest freesurfer release (v.6.0).

These are the versions of some of the programs that are installed on the server:

charcot:~# mnc2nii -version
program: 2.3.01
libminc: 2.3.01
netcdf : 4.3.3 of Feb  8 2016 14:56:05 $
HDF5   : 1.8.15

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
2) Platform: CentOS release 6.8 (Final)
3) uname -a: Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

I have also attached my recon-all log file. If there is anything else I can provide, please let me know.

Thanks,

Muhammad

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.