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

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

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