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
[image: 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 CautionYes, 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 completelywritten, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
MSc Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
