External Email - Use Caution        

Dear Bruce,

On Sun, Nov 18, 2018 at 6:20 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Batuhan

what is the size of the rawavg.mgz file? Can you run mri_info on it?

This is the output I get with mri info on rawavg.mgz:

batuhan@chimere:/auto/data/batuhan/output/BE2/mri$ mri_info rawavg.mgz
Volume information for rawavg.mgz
          type: MGH
    dimensions: 224 x 256 x 176
   voxel sizes: 1.0000, 1.0000, 1.0000
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -112.0, xend: 112.0
        ystart: -128.0, yend: 128.0
        zstart: -88.0, zend: 88.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =   0.0000, y_r =   0.0000, z_r =   1.0000, c_r =     4.1261
              : x_a =  -1.0000, y_a =   0.0000, z_a =   0.0000, c_a =    22.5211
              : x_s =   0.0000, y_s =   1.0000, z_s =   0.0000, c_s =   -11.1121

talairach xfm :
Orientation   : PSR
Primary Slice Direction: sagittal

voxel to ras transform:
                0.0000   0.0000   1.0000   -83.8739
               -1.0000   0.0000   0.0000   134.5211
                0.0000   1.0000   0.0000  -139.1121
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -0.0000  -1.0000  -0.0000   134.5211
               -0.0000  -0.0000   1.0000   139.1121
                1.0000   0.0000   0.0000    83.8739
                0.0000   0.0000   0.0000     1.0000
 
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?


This is how 001.mgz is generated, right after the recon-all command and perl warning:

perl: warning: Falling back to the standard locale ("C").
/auto/data/batuhan/output/BE2

mri_convert /auto/data/batuhan/output/BE2_T1.nii /auto/data/batuhan/output/BE2/mri/orig/001.mgz

mri_convert /auto/data/batuhan/output/BE2_T1.nii /auto/data/batuhan/output/BE2/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/BE2_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/BE2/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Nov 20 17:09:07 +03 2018
Found 1 runs
/auto/data/batuhan/output/BE2/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/BE2/mri/orig/001.mgz /auto/data/batuhan/output/BE2/mri/rawavg.mgz

It cannot load 001.mgz in freeview, but BE2_T1.nii seems fine:

gorkem@friston:~/Desktop$ freeview -v 001.mgz
mghRead(/home/gorkem/Desktop/001.mgz): could not read 229376 bytes at slice 0
MRIread failed: Unable to read from /home/gorkem/Desktop/001.mgz
mghRead(/home/gorkem/Desktop/001.mgz): could not read 229376 bytes at slice 0

Screenshot from 2018-11-20 17-27-03.png
I manually converted anatomical image to 001.mgz on this server, it gave the same error. When I tried it on my desktop, it worked fine. So forth, mri_convert function on the server somehow corrupts nii files. What do you think the reason could be?

Best,
Batuhan
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. <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 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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>
>
> --
>
> 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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-- 
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey