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: [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
