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...