The problem is that the slice thickness is 0. BTW, I don't know what you are planning to do with this in freesurrfer, but it's not going to work with only one slice.

doug

Lisa F. Akiyama wrote:

Hi Doug,

Here's the result of mri_info:

ubuntu:~> mri_info $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii
INFO: using NIfTI-1 qform
Volume information for /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii
         type: nii
   dimensions: 256 x 256 x 1
  voxel sizes: 0.9766, 0.9766, 0.0000
         type: FLOAT (3)
          fov: 250.000
          dof: 0
       xstart: -125.0, xend: -125.0
       ystart: -125.0, yend: -125.0
       zstart: -0.0, zend: -0.0
           TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
      nframes: 1
      PhEncDir: UNKNOWN
ras xform present
   xform info: x_r =   1.0000, y_r =   0.0000, z_r =  -0.0000, c_r =   -11.5117
             : x_a =   0.0000, y_a =  -1.0000, z_a =  -0.0000, c_a =     8.5118
             : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =   -73.1000
Orientation   : RPS
Primary Slice Direction: axial

voxel to ras transform:
               0.9766   0.0000  -0.0000  -136.5116
               0.0000  -0.9766  -0.0000   133.5117
               0.0000   0.0000   0.0000   -73.1000
               0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!


Thank you.

Best,
Lisa
 ______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington

P Please consider the environment before printing this e-mail.

On Thu, Oct 28, 2010 at 4:25 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   mri_info *deface_1433_V1_t1w_slice0.nii

--
Douglas N. Greve, Ph.D.
MGH-NMR Center

greve@nmr.mgh.harvard.edu

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