Hi Doug, Alright. I'll try doing that. Thanks for the information.
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 Mon, Dec 6, 2010 at 7:20 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > There's no easy way to do it. You can convert to a volume and then use the > --slice-crop option in mri_convert to extract out individual slices. > > doug > > Lisa F. Akiyama wrote: > >> Hello, >> >> I have a large number of slice files in ima format. >> I would like to convert each of these ima files into either nifti or >> analyze format slice files. >> I read a past email conversation regarding batch conversion of ima files >> using mri_convert : >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010524.html >> However, when I ran the following commands, I get a single nifti/analyze >> file that contains all the slices for this particular subject. >> Is there a way to batch convert all ima slice files to individual >> nifti/analyze files? >> I read somewhere about the --sdmlist option, but that did not work. >> >> Thanks. >> >> >> Best, >> Lisa >> >> *<ima -> analyze>* >> >> todd $ mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii >> mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii >> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ >> reading from 393-2-4.ima... >> rows = 256 >> cols = 256 >> TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 >> i_ras = (-0, -1, -0) >> j_ras = (-0, 0, -1) >> k_ras = (-1, 0, 0) >> writing to kh4.nii... >> t...@neptune-ubuntu >> :/usr/local/freesurfer/subjects/kikuchi_hiromi/slices$ >> mri_convert -it ima -i 393-2-4.ima -ot analyze -o kh4.img >> mri_convert -it ima -i 393-2-4.ima -ot analyze -o kh4.img >> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ >> reading from 393-2-4.ima... >> rows = 256 >> cols = 256 >> TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 >> i_ras = (-0, -1, -0) >> j_ras = (-0, 0, -1) >> k_ras = (-1, 0, 0) >> writing to kh4.img... >> Analyze Output Matrix >> -0.000 -0.000 -1.500 87.097; >> -1.000 0.000 0.000 114.029; >> -0.000 -1.000 0.000 118.726; >> 0.000 0.000 0.000 1.000; >> -------------------- >> No such orientation specified in Analyze7.5. Set orient to 0 >> Direction cosines for >> /usr/local/freesurfer/subjects/kikuchi_hiromi/slices/393-2-4.ima are: >> x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -4.4032 >> x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = -14.9706 >> x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -10.2740 >> INFO: set hdr.hist.orient to 'transverse unflipped' >> >> >> *<ima -> nifti>* >> >> todd $ mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii >> mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii >> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ >> reading from 393-2-4.ima... >> rows = 256 >> cols = 256 >> TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 >> i_ras = (-0, -1, -0) >> j_ras = (-0, 0, -1) >> k_ras = (-1, 0, 0) >> writing to kh4.nii... >> >> >> ______________________________ >> 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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