External Email - Use Caution
Dear Bruce,
On Sun, Nov 18, 2018 at 6:20 PM Bruce Fischl <fis...@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
[kjFFtSUZ3QnAGUDICTTA_6E7ANwzLBnTF64p_SYi2w0LbngPwmKeldP7AYR8g9kRc-EyfkmKGOfWu83JV6wgu1a-nTU9hIJ_6E
m2o1VJ5WeytUIQM71rTiZBLVk6wxmc3Tf86E9iM1g] 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.
<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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>
>
> --
>
> 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
