Oops...I made an mistake. Should had been: *<ima -> analyze>
*todd$ 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' ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lris...@uw.edu P Please consider the environment before printing this e-mail. On Fri, Dec 3, 2010 at 5:05 PM, Lisa F. Akiyama <lris...@uw.edu> 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 > > P Please consider the environment before printing this e-mail. > >
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