On Wed, Sep 1, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Something went very wrong with the creation of that file. It only has one voxel/vertex.

doug

corinna bauer wrote:

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 <mailto: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
<mailto: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
<mailto: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
<mailto: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
<mailto:fischl@nmr.mgh.harvard.edu>>

fischl@nmr.mgh.harvard.edu
<mailto: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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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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