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 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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
>     gr...@nmr.mgh.harvard.edu <mailto:gr...@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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-- 
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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