Hi Nick
Thanks mris_fix_topology works now!
But i have a similar bug a step later with:
mris_make_surfaces
Can you please check it.
Thans for your help
A
Nick Schmansky wrote:
Abdel,
Indeed mris_fix_topology had the same bug as mris_anatomical_stats (when
running on Slackware Linux). I've posted a fixed version of
mris_fix_topology here:
http://surfer.nmr.mgh.harvard.edu/pub/dist/
named:
mris_fix_topology.gz
mv this to your $FREESURFER_HOME/bin, then type:
gunzip mris_fix_topology.gz
chmod a+x mris_fix_topology
Let me know if you encounter similar bugs. This fixed binary will
appear in the next release.
Nick
On Fri, 2007-01-05 at 14:43 +0000, Abdel Douiri wrote:
Hi Nick
We have done a new update to our Linux system and i have found the same error
that i report a while ago (see bellow) But this time is for mris_fix_topology
program.
Can you please check it again for mris_fix_topology.c file, the error that you found was problem
with sprintf! (sprintf(fname,"%s.mgz",fname) to strcat(fname,".mgz")
).
Thanks
Abdel
Abdel,
Thanks for testing this. The bug fix will appear in an upcoming
release, but you can continue using the mris_anatomical_stats that you
have now.
For those interested in the perils of testing a multi-platform app, the
buggy line of code was:
sprintf(fname,"%s.mgz",fname)
Here the source and destination are the same, which, according to glibc
docs for sprintf, is undefined behavior. The odd thing is that these
Linux variants: RedHat 7.3, RedHat 9, Centos4, Debian and SuSE; and Mac
OS X, all have a shared libc lib that handles the line of code properly.
The libc included with Slackware, however, did not (and understandably
so). libc.so is included not with Freesurfer, but with the OS, so this
means that testing even on a half-dozen different platforms doesn't
guarantee trouble-free performance on a seemingly identical platform.
The proper code in this case is:
strcat(fname,".mgz");
N.
On Fri, 2006-08-18 at 18:40 +0100, A. Douiri wrote:
that s works!
Cheers!
At 01:51 18/08/2006, Nick Schmansky wrote:
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: [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
_______________________________________________
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 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
