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

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On Thu, Dec 2, 2010 at 11:37 AM, Douglas N Greve <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>

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

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