Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

TkmEdit message
by Anil Roy 05 Oct '07

05 Oct '07

Hi, When I run tkmedit, I receive the following message. It doesn't seem to affect the functionality. Could you explain why this message shows up. Xlib: extension "XFree86-DRI" missing on display ":0.0". Thanks, Anil.

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multiple surface overlays
by Cameron Ellis 05 Oct '07

05 Oct '07

Hi all, Sourcing stable3, using tksurfer, does anyone know how to load more than one overlay at a time from the command line? (something like: tksurfer <subject> <hemi> <surface> -overlay1 ??? -overlay2 ??? overlay3 ???) Does this require scripting w/ tksurfer? Cameron

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help on installation under VMWARE + suse 10.2
by Xue,Gui 05 Oct '07

05 Oct '07

hi-I am trying to install freesurfer my computer with the following settings: Operating system: Win XP Open Suse10.2 running under vmware workstation 6.0. Display card: NVIDIA Quadro FX 3400/4400. The problem I have is that the tksurfer doesn't work well, like what's described on the wiki, only small part of the surfer was shown. I updated the display card driver, but it didn't fix the problem. I wonder if anyone has successfully configure the system to make it work. Thanks a lot! gui

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previous FS versions
by Michael Harms 05 Oct '07

05 Oct '07

Hello, Is it possible to get a version of Freesurfer other than the most current? In particular, I'm interested in getting a copy of v3.0.5 for the CentOS (RHEL 4) Linux platform. thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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reference for annotation
by Robert Levy 04 Oct '07

04 Oct '07

Hi, If we use the old version of aparc for parcellation (the older default, as opposed to aparc.a2005s), what should we cite in a paper? Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Re: [Freesurfer] Re: Error: Cannot allocate memory
by Help Desk -- Paul Raines 04 Oct '07

04 Oct '07

Okay, so it is not just CentOS5. But the timestamp on the build is TODAY. So I guess we wait for someone from the freesurfer development team to say something about what changed. On Thu, 4 Oct 2007, Pratap Kunwar wrote: > Yes, here is the info below > ----- > FREESURFER_HOME: /usr/local/freesurfer/stable4 > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071004 > > RedHat release: CentOS release 4.4 (Final) > > Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 > > NMR Center info (/space/freesurfer exists): > > machine: galen > > SUBJECTS_DIR: > /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/ > > PWD: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI > ------------------------------------- > > > Pratap Kunwar <pkunwar(a)nmr.mgh.harvard.edu> > >> What computer are you getting the error on, is it running CentOS5 ? >> >> >> >> Pratap Kunwar wrote: >>> I am also getting the same error as below. >>> >>> >>>> Hi Chris, >>>> >>>> Can you forward me to the person I could ask about this issue? >>>> >>>> I've been running jobs the same way using freesurfer for months and >>>> today >>>> I keep gettting this error message: Cannot allocate memory >>>> >>>> i.e. >>>> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc >>>> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc >>>> TAGskip: failed to calloc 808464384 bytes! >>>> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ >>>> reading from orig.mgz... >>>> Cannot allocate memory >>>> ERROR: converting to minc >>>> Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 >>>> x86_64 x86_64 GNU/Linux >>>> recon-all exited with ERRORS at Thu Oct 4 13:35:24 EDT 2007 >>>> >>>> i.e. >>>> reading >>>> '/usr/local/freesurfer/stable4/average/RB_all_2007-08-08.gca'... >>>> average std = 6.7 using min determinant for regularization = 4.5 >>>> 0 singular and 1985 ill-conditioned covariance matrices regularized >>>> reading 'nu.mgz'... >>>> TAGskip: failed to calloc 842542592 bytes! >>>> Cannot allocate memory >>>> Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 >>>> x86_64 x86_64 GNU/Linux >>>> recon-all exited with ERRORS at Thu Oct 4 13:40:14 EDT 2007 >>>> >>>> >>>> Is there something I can do to fix this problem? >>>> Thanks! >>>> ~Amy >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> On Thu, 4 Oct 2007, Amy DeLuca wrote: >>>>> >>>>> You cab subscribe your self at this URL >>>>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>>> Can you plese add me to the freesurfer email list? >>>>>> >>>>>> Freesurfer Jobs are constantly exiting giving me this error: >>>>>> Cannot allocate memory >>>>>> Thank You >>>>>> >>>>>> ~amy >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> ------------------------------------------------------------------------------- >>>>> Chris Johnson |Internet: johnson(a)nmr.mgh.harvard.edu >>>>> Systems Administrator |Web: >>>>> http://www.nmr.mgh.harvard.edu/~johnson >>>>> NMR Center |Voice: 617.726.0949 >>>>> Mass. General Hospital |FAX: 617.726.7422 >>>>> 149 (2301) 13th Street |Fifty percent of all doctors graduated in >>>>> the >>>>> Charlestown, MA., 02129 USA |lower half of the class. Observation >>>>> ------------------------------------------------------------------------------- >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > > -- --------------------------------------------------------------- Paul Raines email: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA

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Re: [Freesurfer] Re: Error: Cannot allocate memory
by Pratap Kunwar 04 Oct '07

04 Oct '07

I am also getting the same error as below. > Hi Chris, > > Can you forward me to the person I could ask about this issue? > > I've been running jobs the same way using freesurfer for months and today > I keep gettting this error message: Cannot allocate memory > > i.e. > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc > TAGskip: failed to calloc 808464384 bytes! > $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ > reading from orig.mgz... > Cannot allocate memory > ERROR: converting to minc > Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 > x86_64 x86_64 GNU/Linux > recon-all exited with ERRORS at Thu Oct 4 13:35:24 EDT 2007 > > i.e. > reading '/usr/local/freesurfer/stable4/average/RB_all_2007-08-08.gca'... > average std = 6.7 using min determinant for regularization = 4.5 > 0 singular and 1985 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > TAGskip: failed to calloc 842542592 bytes! > Cannot allocate memory > Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 > x86_64 x86_64 GNU/Linux > recon-all exited with ERRORS at Thu Oct 4 13:40:14 EDT 2007 > > > Is there something I can do to fix this problem? > Thanks! > ~Amy > > > > > > >> On Thu, 4 Oct 2007, Amy DeLuca wrote: >> >> You cab subscribe your self at this URL >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> Can you plese add me to the freesurfer email list? >>> >>> Freesurfer Jobs are constantly exiting giving me this error: >>> Cannot allocate memory >>> Thank You >>> >>> ~amy >>> >>> >>> >>> >>> >> >> ------------------------------------------------------------------------------- >> Chris Johnson |Internet: johnson(a)nmr.mgh.harvard.edu >> Systems Administrator |Web: >> http://www.nmr.mgh.harvard.edu/~johnson >> NMR Center |Voice: 617.726.0949 >> Mass. General Hospital |FAX: 617.726.7422 >> 149 (2301) 13th Street |Fifty percent of all doctors graduated in >> the >> Charlestown, MA., 02129 USA |lower half of the class. Observation >> ------------------------------------------------------------------------------- >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: Error: Cannot allocate memory
by Amy DeLuca 04 Oct '07

04 Oct '07

Hi Chris, Can you forward me to the person I could ask about this issue? I've been running jobs the same way using freesurfer for months and today I keep gettting this error message: Cannot allocate memory i.e. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc TAGskip: failed to calloc 808464384 bytes! $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from orig.mgz... Cannot allocate memory ERROR: converting to minc Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:35:24 EDT 2007 i.e. reading '/usr/local/freesurfer/stable4/average/RB_all_2007-08-08.gca'... average std = 6.7 using min determinant for regularization = 4.5 0 singular and 1985 ill-conditioned covariance matrices regularized reading 'nu.mgz'... TAGskip: failed to calloc 842542592 bytes! Cannot allocate memory Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:40:14 EDT 2007 Is there something I can do to fix this problem? Thanks! ~Amy > On Thu, 4 Oct 2007, Amy DeLuca wrote: > > You cab subscribe your self at this URL > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> Can you plese add me to the freesurfer email list? >> >> Freesurfer Jobs are constantly exiting giving me this error: >> Cannot allocate memory >> Thank You >> >> ~amy >> >> >> >> >> > > ------------------------------------------------------------------------------- > Chris Johnson |Internet: johnson(a)nmr.mgh.harvard.edu > Systems Administrator |Web: > http://www.nmr.mgh.harvard.edu/~johnson > NMR Center |Voice: 617.726.0949 > Mass. General Hospital |FAX: 617.726.7422 > 149 (2301) 13th Street |Fifty percent of all doctors graduated in the > Charlestown, MA., 02129 USA |lower half of the class. Observation > ------------------------------------------------------------------------------- > > >

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parcellation problem
by Wang, Xin 04 Oct '07

04 Oct '07

Hello, Group, After I manually removed the skull around cerebellum in the brainmask.mgz, the parcellation of the final inflated brain is totally messed up. Manual corrections of talairach transform and white matter surface did not mess up the parcellation. Could anyone tell me what is wrong? Thank you in advance, Xin Wang

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using the talairach_with_skull.lta transform
by bell0368＠umn.edu 04 Oct '07

04 Oct '07

Hello, We are doing a reproducibility study and have found a different ICV for the same subject. I am trying to check the registration of nu_noneck.mgz to RB_all_withskull_2006-02-15.gca. I believe it is probably a registration problem. Which freesurfer binary would I use to apply the talairach_with_skull.lta transform? Thanks. Chris Bell University of Minnesota

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Freesurfer