Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

thickness maps
by Sasha Wolosin 18 Aug '06

18 Aug '06

Dear all, When I load ?h.thick files as an overlay in tksurfer I notice that values at the thickest points are all listed as having a thickness of exactly 5. Is this a max cutoff in the actual values, or is it just that tksurfer won't display larger values? Is there a better way to visualize thickness files? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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RE: [Freesurfer] problem with mris_anatomical_stats
by A. Douiri 18 Aug '06

18 Aug '06

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: freesurfer-bounces(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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mni_paths
by bdragans＠uke.uni-hamburg.de 18 Aug '06

18 Aug '06

Dear Nick and colleagues, after solving the first problem with nu_correct (fix_mni_paths ... the way you suggested, thanks) we face the fact that the mni paths have to be fixed again after every 2nd, 3rd subject if we try to preprocess a number of subjects data. We run freesurfer with a CentOS 4 version (v3.0.3) on a Windows XP system with VMware and Fedora Core 4. Any suggestions are greatly appreciated... Many thanks Stefan & Bogdan Your last suggestion regarding those issues was: nu_correct is a script which assumes that perl is installed in /usr/bin/perl. If it is not instaled there (and it is by default on centos), then the script fixup_mni_paths will correct the mni scripts to point to your perl path. Also confirm that the environment variables MNI_DATAPATH and MNI_PERL5LIB point into the $FREESURFER_HOME/mni path. You should try running the MNI tools, like nu_correct, and others (see $FREESURFER_HOME/mni/bin) to confirm they work, since there may be some funny interaction with VMWare (but I obviously don't know this just yet). Nick The error is as follows: #@# Nu Intensity Correction Sat Aug 12 09:24:33 BST 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/d/freesurfer/subjects/sub18/mri /mnt/d/freesurfer//bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Sat Aug 12 09:24:33 BST 2006 Setuid/gid script is writable by world. tmpdir is ./tmp.mri_nu_correct.mni.27966 /mnt/d/freesurfer/subjects/sub18/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27966/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27966/nu0.mnc Can't find the talairach xform '/mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -1.46282e-09) j_ras = (7.41336e-09, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.27966/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Aug 12 09:24:42 BST 2006 nu_correct - clobber ./tmp.mri_nu_correct.mni.27966/nu0.mnc ./tmp.mri_nu_correct.mni.27 966/nu1.mnc Setuid/gid script is writable by world. ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Sat Aug 12 09:24:42 BST 2006

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problem with mris_anatomical_stats
by Abdel Douiri 17 Aug '06

17 Aug '06

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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error message regarding mri_ca_register_
by Chacko Cherian 17 Aug '06

17 Aug '06

Hello all, I got this error message while running one of my subjects: ERROR: mri_ca_register with non-zero status Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 14 09:35:29 MST 2006 Does anyone knw wat this could possibly mean? THanks in advance. Chacko Cherian.

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wm and pial edits
by Dziobek, Isabel 17 Aug '06

17 Aug '06

Dear All, I have two short questions concerning edits to the wm and pial surface. 1. if I make edits to both wm and pial surface, can I rerun autorecon2 adding the -wm and -pial flags in one command (i.e. recon-all -autorecon2-wm -autorecon2-pial -s subjname)? 2. I did save as a jpg the inflated surfaces before making edits to the wm and pial surfaces. After rerunning autorecon2 the new inflated surfaces look the same as the old ones (although I see with "tkmedit brainmask.mgz lh.white that my edits were accepted and used to construct differnt wm and pial surfaces). Should I have erased the old inflated surfaces before editing and rerunning? Thanks a lot and regards from Berlin, Isabel

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Skull marrow and skull stripping
by Bo Shi 16 Aug '06

16 Aug '06

Howdy - It seems that the skullstripping step is having some trouble removing bone marrow (see attached image). Adjusting watershed values (I've tried as low as 5) does not make any significant improvement. Does anyone else have this issue? Can anyone provide any hints as to how I might get a better automated skull-strip? I've been manually removing the marrow but it's getting real old. Any thoughts would be much appreciated. Bo

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subject failed autorecon1
by Chacko Cherian 15 Aug '06

15 Aug '06

Hi all, One of my subjects failed autorecon1 giving me this error: mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.646 0.464 -0.179 -16.319; -0.497 0.598 -0.245 -56.371; -0.008 0.303 0.757 179.232; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux zoe 2.6.15-25-386 #1 PREEMPT Wed Jun 14 11:25:49 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Tue Aug 15 16:21:26 MST 2006 Thanks in advance Chacko Cherian

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tkmedit and tksurfer error
by Vishwadeep Ahluwalia 15 Aug '06

15 Aug '06

Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively: tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29 tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64 Please advise! regards, Vish PS: i'm using tksurfer-fc5 as given in the online instructions.

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new .mat reader
by Doug Greve 14 Aug '06

14 Aug '06

Matlab .mat files (as produced by spm, for example) are going to be read into FreeSurfer differently starting tomorrow using code written by Thomas Nommer. The new version should be able to read in matlab5 and matlab4 matrices. This has been a problem with trying to read data produced by newer versions of spm. Tests indicate that there should be no difference between the new and old version, but let us know if you find something strange. This change only applies to the dev environment. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Freesurfer August 2006