Abdel,
I don't think there is a matlab alternative to mris_anatomical_stats.
However, there is a suspicious line of code in mris_anatomical_stats that I have fixed, and I'm wondering if you can give a new binary a try. It is found here:
http://surfer.nmr.mgh.harvard.edu/pub/dist/
and named:
mris_anatomical_stats.gz
To install, after downloading:
gunzip mris_anatomical_stats.gz chmod o+x mris_anatomical_stats mv mris_anatomical_stats $FREESURFER_HOME/bin
While I cannot recreate the error you see, I do not have a Slackware installation, and I am wondering if its core libs are revealing a bug in our code.
Let me know if it works.
Thanks,
Nick
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: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] 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: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] 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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