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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
mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0
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