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.eduwrote:
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
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