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: lris...@uw.edu P Please consider the environment before printing this e-mail. On Thu, Dec 2, 2010 at 11:37 AM, Douglas N Greve <gr...@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: lris...@uw.edu <mailto:lris...@uw.edu> >> >> >> P Please consider the environment before printing this e-mail. >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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