Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh
          type: MGH
    dimensions: 1 x 1 x 1
   voxel sizes: 1.0000, 1.0000, 1.0000
          type: FLOAT (3)
           fov: 1.000
           dof: 1
        xstart: -0.5, xend: 0.5
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees
       nframes: 1
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r = 58340.0000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    11.5254
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     0.0000

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000 58340.5000
                0.0000   0.0000   1.0000    11.0254
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000   0.0000   0.0000 58340.5000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000   -11.0254
                0.0000   0.0000   0.0000     1.0000


On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
can you run

mri_info /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh

and send us the output?


On Wed, 1 Sep 2010, corinna bauer wrote:

mris_anatomical_stats -t
/home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh 1057 lh


On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

what is your full command line?

On Wed, 1 Sep 2010, corinna bauer wrote:

 Then I get this error:

ERROR: number of vertices in
/home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh does not
match surface (1,116670)structure is
"/home/freesurfer4.4.0/subjects/corinna/1057/surf/lh.white"
number of vertices                      = 116670
total surface area                      = 76860 mm^2
total gray matter volume                =  0 mm^3
average cortical thickness              = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature     = 0.131
average integrated rectified Gaussian curvature = 0.112
folding index                           = 2190
intrinsic curvature index               = 223.0


On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:

 Try using the full path to the file



On Sep 1, 2010, at 12:16 PM, corinna bauer <corinnab83@gmail.com> wrote:

Hi Bruce,
When I use the -t flag, I get this message in the output:

mghRead(1057/mri/lh.gwratio.mgh, -1): could not open file

I tried:
mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh 1057 lh

Corinna

On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl <<
fischl@nmr.mgh.harvard.edu>
fischl@nmr.mgh.harvard.edu> wrote:

 Hi Corinna,

the gwratio.mgh is a scalar field over the surface, *not* a surface
(i.e.
it has no topology information). Try:

mris_anatomical_stats -t lh.gwratio.mgh

and the rest as normal. Note that it will report the values as
"thickness"

cheers
Bruce



On Mon, 30 Aug 2010, corinna bauer wrote:

 I am trying to get an output with average gray/white ratio values for

each
segmentation. I tried using the gwratio.mgh file as the input for
mris_anatomical_stats, but got the following error message:

reading input surface
/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh...
ERROR: MRISread: file
'/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0
vertices!

Any insight?



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