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: lris...@uw.edu P Please consider the environment before printing this e-mail. On Thu, Dec 2, 2010 at 4:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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: lris...@uw.edu <mailto: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 <mailto: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> >> <mailto: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 >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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. >> >> >> > -- > 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 > >
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