Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30079 discussions

preproc-sess failure on Mac
by Shigeaki Nishina 08 Oct '07

08 Oct '07

I'm trying to use freesurfer/fsfast on Mac Pro and found preproc-sess fails in mcparams2etreg. The problem seems actually in Mac version of MATLAB, which does not terminate properly when it finishes processing the piped code without an explicit 'exit' at the end of it (I asked Mathworks and confirmed this is a bug existing in all MATLAB versions for Mac OS X). Because the MATLAB process does not quit, mcparams2etreg can not continue processing the rest. A workaround for this problem is to put a wrapper script that calls matlab after adding 'exit' at the end of the piped code, with the name of 'matlab' in the shell path. Is this a known issue? -- Shigeaki Nishina

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Question on fs-fast
by lan lin 08 Oct '07

08 Oct '07

I'm trying to use fs-fast to analysis the PET data, but found that the first level analysis is specially designed for fmri. Is there any way to use fs-fast to analysis the PET data?

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selxavg-sess error
by raij＠nmr.mgh.harvard.edu 08 Oct '07

08 Oct '07

Hi Doug, selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus exits with the error: ... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -------------- ??? Error using ==> minus Matrix dimensions must agree. Error in ==> fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs. Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects. (Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis) Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge. machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Thanks!!! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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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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