until we fix mri_convert to read your dicoms, you can also add direction cosine info to the mri_convert command-line, although it's not very intuitive. something like:

mri_convert 001.img 001 -iid -1 0 0 -ijd 0 -1 0 -ikd 0 0 1

-iid, -ijd, and -ikd indicate the direction cosines for the fastest, next fastest, and slowest dimension. The three values indicate the RAS.
eg, -1 0 0 means that R decreases with index. You can play around with these. Bring the result up in tkmedit to see if it is oriented correctly. For the given orientation, it should look like the picture in the little button. The only thing you can't tell is left-right. From the direction cosine below, it looks like it should be -iid -1 0 0.

doug

Glenn Lawyer wrote:

Hi,

We are also seeing the segmentation fault when running mri_convert on our dicom files. As a work-around, I have written a script that uses xmedcon to batch convert dicom to analyze. I'm planning on posting the script to this list, but want to resolve one little issue first.

When I run mri_convert on the resulting analyze files, the COR images are in axial orientation. This is probably because the command"$mri_convert 001/001.img ."
"Could not find the direction cosine information. Will use the HORIZONTAL orientation.
If not suitable, please provide the information in 001/001.mat file".

I want to modify my script so that it creates the .mat file, but do not know the format.

I can extract the directional cosine information using dicom2 (dicom2 -t1 001/IMAGE_1.dcm | grep Orientation), giving me
Image Orientation (Patient) (0020,0037) 6 DS [0.999848\0.00778219\0.0156255\0.0156255\0.00012207\-0.999878]

Could you kindly send me the appropriate 001.mat file for this subject/aquisition?

+glenn
-- 

I want to go farther, farther!

          A. E. L.

>  Glenn Lawyer                   <
>  +352 061 967 244               <
>  Instituttgruppe for psykiatri  <
>  Postboks 1130 Blindern         < 
>  0318 Oslo                      <
<  http://folk.uio.no/davidgl     >
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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