New subject: mri_glmfit allocate memory error

6 Jun 2012

      What is your command-line and what is the terminal output? Also, please
post to the list instead of to me directly.
thanks
doug
On 6/6/12 5:24 AM, lordowen wrote:
...
Dear Prof. Greve:
Sorry to reply this very old post, but we encountered the same
problem. We processed our data following the instructions in
PairedAnaylsis page on Wiki. Everything is fine but we can't perform
mri_glmfit using command-line. So we need your advise to seek possible
solutions for this problem.
We are using FS 5.1 under Mac OS 10.7.4. We have 12GB memory and about
500GB HD space.
Thanks you for your kindly help.
2011/3/16 Douglas N Greve greve@nmr.mgh.harvard.edu:
...
So you re-ran mris_preproc and you still get the error? If so, try running
mris_preproc --debug <Your Options> |& tee mris_preprog.err.log
Send me the mris_preprog.err.log, but don't email it as it will likely
be huge. Instead drop it to me a the file drop listed at the end of this
email.
doug
Andrew Mendlowitz wrote:
...
The mri_prepoc runs fine still but the glmfit still says can not
allocate memory, there is 8gb of ram and very little disk space is
used up, there is 876.1 gb still free.
On Fri, Mar 11, 2011 at 12:49 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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>
    <mailto: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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_glmfit allocate memory error