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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. < DGREVE@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 CautionHello,
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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