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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
