Hi Nick,
Thanks in advance for your help and i would like to ask is there an
alternative in matlab for example to do mris_anatomical_stats?
The detail of the outjkputs is:
the output of:
$ mris_anatomical_stats --all-info
ProgramName: mris_anatomical_stats ProgramArguments: --all-info
ProgramVersion: $Name: stable3 $ TimeStamp: 06/08/17-10:28:55-GMT CVS: $Id:
mris_anatomical_stats.c,v 1.35.2.1 2006/04/21 19:45:19 nicks Exp $ User:
douiri Machine: img-179 Platform: Linux PlatformVersion: 2.6.16.22
CompilerName: GCC CompilerVersion: 30400
I tried with other subjects and also bert and i get the same problem:
$ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a
../label/lh.aparc.annot -c ../stats/aparc.annot.ctab bert lh
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume .mgz...
zcat: /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: No
such file or directory
mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, -1):
read error
mris_anatomical_stats: could not read input volume .mgz
the freesurfer version
$ cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos4-stable-pub-v3.0.3
and the linux version is:
$ cat /etc/slackware-version
Slackware 10.2.0
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky
Sent: 17 August 2006 00:06
To: Abdel Douiri
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] problem with mris_anatomical_stats
Abdel,
This problem is truly strange. The filename seems to just disappear.
Can you send me the output of:
mris_anatomical_stats --all-info
Also, does this error repeat? That is, if you try:
cd $SUBJECTS_DIR/01_00/scripts
mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats \
-b -a ../label/lh.aparc.annot \
-c ../stats/aparc.annot.ctab 01_00 lh
does it fail again? And does this happen for other subjects?
Also, which freesurfer version is being used? To find out, type:
cat $FREESURFER_HOME/build-stamp.txt
And which Linux OS is it installed upon?
Nick
On Wed, 2006-08-16 at 17:16 +0100, Abdel Douiri wrote:
> Thanks Bruce
> I have put the subject and that is "01_00" and the first and second
> autorecon was OK only the autorecon3 where it was the problem. Attached
the
> log file.
> Thanks a lot for your help
> Abdel
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl
> Sent: 16 August 2006 14:01
> To: Abdel Douiri
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] problem with mris_anatomical_stats
>
> Hi Abdel,
>
> is that the full command line? If so, you need to specify a subject with
> -subjid. If not, could you send us the full command line and
recon-all.log?
>
> cheers,
> Bruce
>
>
> On Wed, 16 Aug 2006, Abdel Douiri wrote:
>
> > Hi all,
> >
> >
> >
> > I will be grateful if someone can tell me what going wrong in the
> following
> > problem:
> >
> > When running "recon-all -autorecon3" the program stop with error exactly
> in
> > the "mris_anatomical_stats" cmd stage and I have the following error:
> >
> >
> >
> > mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a
> > ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab 01_00 lh
> >
> >
> >
> > computing statistics for each annotation in ../label/lh.aparc.annot.
> >
> > reading volume .mgz...
> >
> > zcat: /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz:
> No
> > such file or directory
> >
> > mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz,
> -1):
> > read error
> >
> > mris_anatomical_stats: could not read input volume .mgz
> >
> > INFO: assuming MGZ format for volumes.
> >
> > Linux img-179 2.6.16.22 #2 SMP Mon Jun 26 15:49:31 BST 2006 i686 unknown
> > unknown GNU/Linux
> >
> >
> >
> > recon-all exited with ERRORS at Tue Aug 15 20:52:49 BST 2006
> >
> >
> >
> >
> >
> > Thanks
> >
> > A
> >
> >
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