Hi Batuhan
what is the size of the rawavg.mgz file? Can you run mri_info on it? How
did you create the 001.mgz? Rerunning recon-all won't help if the 001.mgz
is already corrupted - you will need to regenerate it. That fact that we
can't even read slice 0 suggests there is something badly wrong with it.
Can you look at it in freeview?
cheers
Bruce
On Sat, 17 Nov 2018, Batuhan Erkat wrote:
External Email - Use Caution
Yes, unfortunately same error reoccurs in three different machines. I talked
with some people at the
research center, they claimed that it could be due to high load. However, I
tried again while the
average load was at 5% (via top command), the issue persists. Do you have any
clue what might be the
underlying problem? A necessary bug fix we could have missed etc.?
Batuhan
On Sat, Nov 17, 2018 at 12:11 AM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu> wrote:
Probably it was interrupted and the file as not completely written, or
you ran out of
space on the disk. If you start over, does it continue to happen?
On 11/16/18 4:15 PM, Batuhan Erkat wrote:
External Email - Use Caution
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
--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
_______________________________________________
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