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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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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---

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