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 $reading from /auto/data/batuhan/output/BE/mri/rawavg.mgz...Invalid argument* Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s BE exited with ERRORS at Fri Nov 16 23:43:50 +03 2018
For more details, see the log file /auto/data/batuhan/output/BE/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thank you. Best regards, O. Batuhan Erkat
Probably it was interrupted and the file as not completely written, or you ran out of space on the disk. If you start over, does it continue to happen?
On 11/16/18 4:15 PM, Batuhan Erkat wrote:
External Email - Use Caution
Hello,
I am using FreeSurfer solely for reconstruction. I am having an issue I didn't have a month ago, right at the beginning of reconstruction pipeline. I am using FreeSurfer v5.3.0 on an Ubuntu 14.04 server. Based on some search and thinking, I guess that mghread is not able to read rawavg.mgz either there is a bug with the mghread or the data gets corrupted during mri_convert, because when I inspect the T1.nii images, there seems to be nothing wrong. Furthermore, I tried recon-all command on the anatomical images I reconstructed a month ago without any error (which means they were totally okay), but not surprisingly I received the same error message when I tried to conduct recon-all on them: mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0 I also included an error log, and the full terminal output where I bolded out the problematic lines. Also, I am not sure how related it is with my issue but there are some warnings from perl as well.
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /auto/data/batuhan/output MNI_DIR /usr/local/freesurfer/mni batuhan@chimere:~$ 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
Hi Batuhan
what is the size of the rawavg.mgz file? Can you run mri_info on it? 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?
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
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
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
wow, I have no idea. Can you send us the .nii file and we will try? What machine is it failing on and does it print any error messages during conversion? Can you send us the full command line and terminal output of the mri_convert command that fails?
cheers Bruce On Tue, 20 Nov 2018, Batuhan Erkat wrote:
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
[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. <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 > > > _______________________________________________ > 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--
MSc Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey
freesurfer@nmr.mgh.harvard.edu
-
Batuhan Erkat -
Bruce Fischl -
Greve, Douglas N.,Ph.D.