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