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


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--
Albert
Lab of Complex System and Artificial Intelligence,
Institute of Automation,Chinese Academy of Sciences(CASIA)
Beijing, 100190,P.R.CHINA