Hello,

I am using FreeSurfer solely for reconstruction. I am having an issue I didn't have a month ago, right at the beginning of reconstruction pipeline. I am using FreeSurfer v5.3.0 on an Ubuntu 14.04 server. Based on some search and thinking, I guess that mghread is not able to read rawavg.mgz either there is a bug with the mghread or the data gets corrupted during mri_convert, because when I inspect the T1.nii images, there seems to be nothing wrong. Furthermore, I tried recon-all command on the anatomical images I reconstructed a month ago without any error (which means they were totally okay), but not surprisingly I received the same error message when I tried to conduct recon-all on them: mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0

I also included an error log, and the full terminal output where I bolded out the problematic lines. Also, I am not sure how related it is with my issue but there are some warnings from perl as well.

-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /auto/data/batuhan/output
MNI_DIR           /usr/local/freesurfer/mni
batuhan@chimere:~$ recon-all -i /auto/data/batuhan/output/BE_T1.nii -s BE -all
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /auto/data/batuhan/output
Actual FREESURFER_HOME /usr/local/freesurfer
Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = "en_US:en",
    LC_ALL = (unset),
    LC_PAPER = "tr_TR.UTF-8",
    LC_ADDRESS = "tr_TR.UTF-8",
    LC_MONETARY = "tr_TR.UTF-8",
    LC_NUMERIC = "tr_TR.UTF-8",
    LC_TELEPHONE = "tr_TR.UTF-8",
    LC_IDENTIFICATION = "tr_TR.UTF-8",
    LC_MEASUREMENT = "tr_TR.UTF-8",
    LC_TIME = "tr_TR.UTF-8",
    LC_NAME = "tr_TR.UTF-8",
    LANG = "C"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
/auto/data/batuhan/output/BE

 mri_convert /auto/data/batuhan/output/BE_T1.nii /auto/data/batuhan/output/BE/mri/orig/001.mgz

mri_convert /auto/data/batuhan/output/BE_T1.nii /auto/data/batuhan/output/BE/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /auto/data/batuhan/output/BE_T1.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to /auto/data/batuhan/output/BE/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fri Nov 16 23:43:47 +03 2018
Found 1 runs
/auto/data/batuhan/output/BE/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /auto/data/batuhan/output/BE/mri/orig/001.mgz /auto/data/batuhan/output/BE/mri/rawavg.mgz

/auto/data/batuhan/output/BE

 mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz /auto/data/batuhan/output/BE/mri/orig.mgz --conform

mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz /auto/data/batuhan/output/BE/mri/orig.mgz --conform
mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /auto/data/batuhan/output/BE/mri/rawavg.mgz...
Invalid argument
Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s BE exited with ERRORS at Fri Nov 16 23:43:50 +03 2018

For more details, see the log file /auto/data/batuhan/output/BE/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thank you.

Best regards,

O. Batuhan Erkat