Hi, I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time. However, I get this error about the mghRead as follows.
*~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/** liwentao_1.mgz* Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 31 09:20:08 CST 2009
I try to run it step by step: *~$ mri_convert /mnt/data2/data/trauma/**liwentao_1.mgz /usr/local/freesurfer/**subjects/liwentao_1/mri/orig/**001.mgz* mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38
There is sufficient disk space for freesurfer running. I searched the mail-archive and noticed the potential solutions. But it doesn't work.
Any suggestion is appreciated!
does mri_convert work on the sample data? that is:
cd $FREESURFER_HOME/subjects/bert/mri mri_convert orig.mgz test.mgz
if it does, then there is something wrong with your file 'liwentao_1.mgz'.
Nick
On Fri, 2009-07-31 at 09:51 +0800, leemon albert wrote:
Hi, I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time. However, I get this error about the mghRead as follows.
~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/liwentao_1.mgz Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 31 09:20:08 CST 2009
I try to run it step by step: ~$ mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38
There is sufficient disk space for freesurfer running. I searched the mail-archive and noticed the potential solutions. But it doesn't work.
Any suggestion is appreciated!
-- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What if you rename the file liwentao_1.mgz to liwentao_1.mgh.gz
mv liwentao_1.mgz liwentao_1.mgh.gz
and gunzip it
gunzip liwentao_1.mgh.gz
this should work. If this doesn't work, it means the file is corrupted.
If it works, use the resulting file "liwentao_1.mgh" as an input to recon-all
recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/ liwentao_1.mgh
Cheers Krish
On Jul 30, 2009, at 11:24 PM, Nick Schmansky wrote:
does mri_convert work on the sample data? that is:
cd $FREESURFER_HOME/subjects/bert/mri mri_convert orig.mgz test.mgz
if it does, then there is something wrong with your file 'liwentao_1.mgz'.
Nick
On Fri, 2009-07-31 at 09:51 +0800, leemon albert wrote:
Hi, I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time. However, I get this error about the mghRead as follows.
~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/liwentao_1.mgz Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/ freesurfer/subjects/liwentao_1/mri/orig/001.mgz
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/ freesurfer/subjects/liwentao_1/mri/orig/001.mgz mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 31 09:20:08 CST 2009
I try to run it step by step: ~$ mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/ freesurfer/subjects/liwentao_1/mri/orig/001.mgz mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/ freesurfer/subjects/liwentao_1/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38
There is sufficient disk space for freesurfer running. I searched the mail-archive and noticed the potential solutions. But it doesn't work.
Any suggestion is appreciated!
-- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA
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
Thanks for your help. First, I tried Nick's method. ~$ cd $FREESURFER_HOME/subjects/bert/mri /usr/local/freesurfer/subjects/bert/mri$ ls aparc.a2005s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz rawavg.mgz .... /usr/local/freesurfer/subjects/bert/mri$ *mri_convert orig.mgz test.mgz* mri_convert orig.mgz test.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from orig.mgz... mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/bert/mri/orig.mgz',frame -1,errno=38 (the same problem)
Second, I tried Krish's method. /usr/local/freesurfer/subjects/bert/mri$ *mv orig.mgz orig.mgh.gz* /usr/local/freesurfer/subjects/bert/mri$ *gunzip orig.mgh.gz* /usr/local/freesurfer/subjects/bert/mri$ ls aparc.a2005s+aseg.mgz orig aparc+aseg.mgz orig.mgh /usr/local/freesurfer/subjects/bert/mri$ *recon-all -autorecon1 -s liwentao_1 -i /usr/local/freesurfer/subjects/bert/mri/orig.mgh * Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig.mgh /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig.mgh /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz *mghWrite(/usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz, -1): gzip had error* $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz... *ERROR: failure writing /usr/local/freesurfer/subjects/liwentao_1/mri/orig* /001.mgz Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 31 14:15:27 CST 2009
The file permissions is displayed as followed: /usr/local/freesurfer/subjects/bert/mri$ ls -l /usr/local/freesurfer/subjects/ total 19471 drwxr-xr-x 12 nica nica 336 2009-03-08 01:01 bert drwxr-sr-x 6 nica nica 168 2008-11-12 05:12 V1_average drwxrwsr-x 12 nica nica 368 2009-07-31 14:15 liwentao_1 drwxrwsr-x 12 nica nica 368 2009-07-17 15:06 dinghai drwxrwsr-x 12 nica nica 336 2009-07-22 14:25 dinghai_4 drwxrwsr-x 12 nica nica 336 2009-07-03 11:11 dinghai-69 drwxr-sr-x 8 nica nica 192 2007-08-15 05:40 fsaverage .... /usr/local/freesurfer/subjects/bert/mri$ ls -l /usr/local/freesurfer/subjects/liwentao_1/ total 4 drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 bem -rw-rw-r-- 1 nica nica 89 2009-07-31 14:20 error.log drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 label drwxrwsr-x 4 nica nica 104 2009-07-31 14:20 mri drwxrwsr-x 2 nica nica 312 2009-07-31 14:20 scripts drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 src drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 stats drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 surf drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 tmp drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 touch drwxrwsr-x 2 nica nica 48 2009-07-31 14:20 trash
Maybe the core of problem is failure writing(including *mghWrite*), but why there is writing error and how to fix it?
Best Regards!
On Fri, Jul 31, 2009 at 11:43 AM, Krish Subramaniam < krish@nmr.mgh.harvard.edu> wrote:
What if you rename the file liwentao_1.mgz to liwentao_1.mgh.gz
mv liwentao_1.mgz liwentao_1.mgh.gz
and gunzip it
gunzip liwentao_1.mgh.gz
this should work. If this doesn't work, it means the file is corrupted.
If it works, use the resulting file "liwentao_1.mgh" as an input to recon-all
recon-all -autorecon1 -s liwentao_1 -i
/mnt/data2/data/trauma/liwentao_1.mgh
Cheers Krish
On Jul 30, 2009, at 11:24 PM, Nick Schmansky wrote:
does mri_convert work on the sample data? that is:
cd $FREESURFER_HOME/subjects/bert/mri mri_convert orig.mgz test.mgz
if it does, then there is something wrong with your file 'liwentao_1.mgz'.
Nick
On Fri, 2009-07-31 at 09:51 +0800, leemon albert wrote:
Hi, I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time. However, I get this error about the mghRead as follows.
~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/liwentao_1.mgz Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz
mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 31 09:20:08 CST 2009
I try to run it step by step: ~$ mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38
There is sufficient disk space for freesurfer running. I searched the mail-archive and noticed the potential solutions. But it doesn't work.
Any suggestion is appreciated!
-- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA
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
freesurfer@nmr.mgh.harvard.edu
-
Krish Subramaniam -
leemon albert -
Nick Schmansky