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