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 ProgramNational Magnetic Resonance Research Center
> (UMRAM) &Aysel Sabuncu Brain Research Center
> Bilkent UniversityAnkara, 06800Turkey
>
>
>
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--
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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