Re: [Freesurfer] Saving individual slices within a nifti file

Hi Doug,

Thanks for the tips. It is working now.

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 4:13 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

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

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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>>



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