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...
   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 <mailto:lrisa87@uw.edu>

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