You would have to take all 45 slices and put them into one volume. It won''t work slice-by-slice. It is probably the case that this won't work either as we usually use high res data. For intensity normalization, maybe it will work.

doug

Lisa F. Akiyama wrote:

Hi Doug,

There are approximately 40~45 slices of each individual's brain,
each saved as separate nifti files.
I'm trying to use FreeSurfer for the Non-uniform intensity normalization and skull strip functions.
So, if I edit the header of each nifti file so that the slice thickness isn't 0,
recon-all -autorecon1 should work?

Thanks.

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 Fri, Oct 29, 2010 at 10:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   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>
       <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
   Phone Number: 617-724-2358 Fax: 617-726-7422

   Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

   <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

   FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

   <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

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   whom it is
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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