Freesurfer October 2007

freesurfer@nmr.mgh.harvard.edu

55 participants
79 discussions

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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autorecon1 error
by Xiangchuan Chen 03 Oct '07

03 Oct '07

Hi all, I have got the following error message when running "recon-all -autorecon1" with one of my subject's data: SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. ... recon-all exited with ERRORS at ... Could anybody tell me how to resolve this issue? Thanks in advance, Xiangchuan Chen

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Segmentation of MRI with cortical lesions
by Martti Ilvesmäki 02 Oct '07

02 Oct '07

Hi, I'm using Freesurfer to generate the necessary surface-files for MNE software. However, when using the automatic segmentation on MRI from patients with cortical lesions, the segmentation does not work correctly. In one case the pial matter surface forms a deep hole (several cm) into the cortex at the location of the lesion. In another case the generated pial matter surface runs approximately along the surface or the white matter and the generated white matter surface seems blurred, with no distinct connection to the anatomy. What would be the easiest way to correctly segment these images? Or is there no simple way? Thanks in advance, Martti Ilvesmäki

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loading surface as a weighted graph
by Michael Harms 02 Oct '07

02 Oct '07

Hello, This question is directed to the universe of FS users: Has anyone created a set of tools (e.g., Matlab) for converting FS surfaces into a (sparse) weighted graph structure? In principle, it doesn't seem like this will be too difficult to implement (making use of the some of the existing FS/Matlab 'read' functions that are already available). But, if anyone already has existing code that they are willing to share, I'd appreciate hearing from you. cheers, 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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RE: [Freesurfer] automated parcellation: training set of Freesurfer
by "Woo Suk, Tae" 02 Oct '07

02 Oct '07

Dear Dr Bruce Fischl. How are you? I preprocessed 41 subjects' MRI to measure the volumes of the cortical and subcortical structures with ver 3.04 Freesurfer. What kind of atlas (Desikan-Killiany atlas or Destrieux atlas?) was used for my data? And how can I choose the atlas between the two atlases. If you provide me the tool for new training set, I'd like to create my own study specific atlas. Really thank for your reply! Sincerely Woo Suk, Tae -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 9:03 PM To: Woo Suk, Tae Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] automated parcellation: training set of Freesurfer there are two training sets we use for the two difference parcellation schemes. Once consists of about 40 subjects distributed into 4 groups (young, middle aged, elderly and Alzheimer's for the Desikan-Killiany atlas). The other is 14 young and middle aged subjects in the Destrieux atlas. Defining a new training set is extremely labor intensive, but we distrubute tools for you to do so if you decide to. cheers, Bruce On Mon, 1 Oct 2007, Woo Suk, Tae wrote: > Dear experts. > > In the previous technical papers of Freesurfer, the the method of automated parcellation was described, > > "This procedure automatically assigns a neuroanatomical label to each voxel > in an MRI volume based on probabilistic information automatically estimated > from manually labeled training set." > > I'd like to know more detail, how many training set was used in Freesurfer, > and is it possible to define the study specific training set for automated parcellation using Freesurfer? > > Sincerely > > Woo Suk, Tae > Seoul, Korea > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Freesurfer October 2007