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
