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... todd@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: lrisa87@uw.edu
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