does average_305_test_slice0.nii not exist? Do you have write perms to that dir? I just tried it here, and it works

doug

Lisa F. Akiyama wrote:

Hi Doug,

Thanks for the tip.
I ran the following command, but no output was created:

   todd: mri_convert -i
   $SUBJECTS_DIR/mni305_minc/average_305_test.nii --slice-crop 0 154
   -o $SUBJECTS_DIR/mni305_minc/average_305_test_slice0.nii
   mri_convert -i
   /usr/local/freesurfer/subjects/mni305_minc/average_305_test.nii
   --slice-crop 0 154 -o
   /usr/local/freesurfer/subjects/mni305_minc/average_305_test_slice0.nii

   $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
   reading from
   /usr/local/freesurfer/subjects/mni305_minc/average_305_test.nii...
   Cropping slices from 0 to 154
   TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
   i_ras = (1, 0, 0)
   j_ras = (0, 1, 0)
   k_ras = (0, 0, 1)
   writing to
   /usr/local/freesurfer/subjects/mni305_minc/average_305_test_slice0.nii...

Could you guide me on what I am doing wrong?

Thanks.


Best,
Lisa
 ______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
Portage Bay Building, BOX 357988
Seattle, WA 98195-7988  U.S.A.

E-mail: lrisa87@uw.edu <mailto:lrisa87@uw.edu>

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

On Thu, Dec 2, 2010 at 11:37 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   Try the --slice-crop option

   doug

   Lisa F. Akiyama wrote:

       Hello,

       Is there a way to individually save slices within a nifti file
       in the nifti format
       using the mri_convert command?

       Thank you.


       Best,
       Lisa
        ______________________________
       Lisa F. Akiyama
       Research Study Assistant
       Institute for Learning & Brain Sciences (I-LABS)
       University of Washington
       E-mail: lrisa87@uw.edu <mailto:lrisa87@uw.edu>

       <mailto:lrisa87@uw.edu <mailto:lrisa87@uw.edu>>

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

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