If you re-run mris_preproc does the same thing happen? Are you running out of disk space? doug

Andrew Mendlowitz wrote:

The code for the lh.paired-diff.thickness.mgh file is mris_preproc --target fsaverage --hemi lh \

--meas thickness --out lh.paired-diff.thickness.mgh \

--fsgd pairss.fsgd --paired-diff

On Thu, Mar 10, 2011 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

There appears to be something wrong with the
lh.paired-diff.thickness.mgh file. How was it created?
doug

Andrew Mendlowitz wrote:

    Hello All,
    I get the following error while trying to run mri_glmfit. I am
    running a 2.93 ghz imac with 8gb of ram. I am also running
    freesurfer version 5.0.0 on Snow
    Leopard OS version 10.6.


     /Applications/freesurfer/subjects/qdec$  mri_glmfit  --glmdir
    lh.paired-diff --fsgd paired-diff.fsgd  --C mean.mtx --y
    lh.paired-diff.thickness.mghgdfReadHeader: reading
    paired-diff.fsgd
    INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
    Continuous Variable Means (all subjects)
    0 Age 1.5
    Class Means of each Continuous Variable
    1 Main   1.5000
    INFO: gd2mtx_method is dods

    $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
    cwd /Applications/freesurfer/subjects/qdec
    cmdline mri_glmfit --glmdir lh.paired-diff --fsgd
    paired-diff.fsgd --C mean.mtx
    --y lh.paired-diff.thickness.mgh
    sysname  Darwin
    hostname larry
    machine  i386
    user     amend
    FixVertexAreaFlag = 1
    UseMaskWithSmoothing     1
    OneSampleGroupMean 0
    y  
     /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
    logyflag 0
    usedti  0
    FSGD paired-diff.fsgd
    glmdir lh.paired-diff
    IllCondOK 0
    DoFFx 0
    Creating output directory lh.paired-diff
    Loading y from
    /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
    mri_glmfit(79576) malloc: *** mmap(size=2563764224) failed
    (error code=12)
    *** error: can't allocate region
    *** set a breakpoint in malloc_error_break to debug
    MRIallocIndices: could not allocate 1714511945 elt index array
    Cannot allocate memory

    The mri_info for the file is :

    mghRead(/Applications/freesurfer/subjects/qdec/fsgd_input.mgh,
    -1): could not
    open file
    amend@larry /Applications/freesurfer/subjects/qdec$  mri_info
    /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
    Volume information for
    /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
             type: MGH
       dimensions: 1714510945 x 1853057372 x 1634628457 x 1668310833
      voxel sizes: 72950800688805540228332034981888.0000, 0.0000,
    70387746064971392794503413760.0000
             type: UNKNOWN (842347100)
              fov: inf
              dof: 1668244335
           xstart: -inf, xend: inf
           ystart: -39.8, yend: 39.8
           zstart: -57528904905339976080461439864148066304.0, zend:
    57528904905339976080461439864148066304.0
               TR: 71446969504754118412748034408448.00 msec, TE:
    17862977898376175754203558313984.00 msec, TI:
    4464583905807213894543171649536.00 msec, flip angle:
    4128358109894647822155776.00 degrees
          nframes: 1668310833
          PhEncDir: UNKNOWN
    ras xform present
       xform info: x_r = 19441367164500690594879212879872.0000, y_r =
    282670772483715414097920.0000, z_r =
    4630517930517356511053742080.0000, c_r =
    18179207505345150839094025125888.0000
                 : x_a = 72953300747400503281465327353856.0000, y_a =
    71756401321839400437789128392704.0000, z_a =
    4721224652433019196440490016768.0000, c_a =     0.0000
                 : x_s =   0.0000, y_s =
    208210237828607676252160.0000, z_s =
    4286666299869639999488.0000, c_s =
    4622889417339745644740714954752.0000

    talairach xfm :
    Orientation   : AAA
    Primary Slice Direction: coronal

    voxel to ras transform:
                      inf 12133604733747200.0000      inf       -inf
                      inf 3080133850722982464323584.0000      inf
          -inf
                 36752183205510726549504.0000
    8937395835633664.0000      inf      -inf
                   0.0000   0.0000   0.0000     1.0000

    voxel-to-ras determinant nan

    ras to voxel transform:
    mat = NULL!
    Invalid argument
    MatrixFree: NULL mat POINTER!

    Invalid argument

    -Andrew
    ------------------------------------------------------------------------

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-- 
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>
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



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