Re: [Freesurfer] problem with selxavg3

The new version is much different, and you can't run 4.5 analyses on 5.1. It does not run mri_fwhm by default, so that will help. If you want to continue to use 4.5, then try --no-fwhm. doug

Maryam Vaziri Pashkam wrote:

Thanks Doug,

I am not running out of space. I did delete the analysis and it did not help. Anyhow, I jsut upgraded my freesurfer to freesurer 5.1 to see if the issue is resolved with the new version.

Maryam

On Mon, Aug 29, 2011 at 11:29 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Maryam, it looks like there is a corrupted file there. Did you
run out of space on your disk? If not, have you tried to delete
the analysis and rerun? You might also try adding -no-fwhm (I
can't remember if 4.5 takes this option).
doug


Maryam Vaziri Pashkam wrote:

    Hi,

    I am encountering a memory allocation error with selxavg3-sess
    and I am not sure how to get around it:

    Here is the lines that I am running
    mkanalysis-sess -analysis FHPDM_noauto -TR 2 -paradigm
    allpara.par -designtype event-related -funcstem fmc -motioncor
    -runlistfile FHPDM_runlist.txt -inorm -nconditions 8
    -timewindow 20 -TER 2 -polyfit 2 -mcextreg -noautostimdur -force

    selxavg3-sess -s 110821_xu_FHPDM_02 -df sessdir -analysis
    FHPDM_noauto
    It is a single subject data with 12 runs, event related design
    that each event last for about 4 seconds and the total
    experiment time is 328 seconds( at TR=2 is equal to 164 TRs)

    My computer is a MAC with 4 gb of ram. and I am running
    freesurfer 4.5. I have ran similar analysis on the same number
    of runs but much longer events (12 sec) before and have not
    had a problem. This is the first time I am analyzing data for
    this particular experiment though.
    Here is the error line that I get:

    mri_fwhm(2138) malloc: *** mmap(size=16777216) failed (error
    code=12)
    *** error: can't allocate region
    *** set a breakpoint in malloc_error_break to debug
    MRIalloc(70, 70, 33): could not allocate 19600 bytes for
    49364th slice

    voxelvolume 35.3062 mm3
    Loading mask
    /Users/maryam/mri-space/studies/FHPDM/unpackdata/110821_xu_FHPDM_02/bold/FHPDM_noauto/mask.nii
    Search region is 60647 voxels = 2141216.616840 mm3
    Polynomial detrending, order = 0
    Detrending
    Cannot allocate memory
    [dhcp-0170571539-df-00:st

    Can anyone help?
    Thanks,
    Maryam


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
<tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.