The direction cosines (DCs) for the row, col, and slice.
The DCs for the row and column are obtained from DICOM (20,37),
which is a string of the form "cx\cy\cz\rx\ry\rz". The slice DC is
obtained from the ASCII header. The x, y, and z components are from
three lines of the form "sSliceArray.asSlice[0].sNormal.dAAA" where
AAA is Sag (x), Cor (y), and Tra (z). Siemens may reverse the slice
order in order to make the images more readable by
radiologists. This reversal is NOT accompanied by a change the
slice direction cosine. Rather, it is indicated by the presence of
sSliceArray.ucImageNumbAAA (any of the three). The FreeSurfer
software reverses the slices upon read-in rather than chaning
the direction cosine.
On 1/10/2022 12:22 PM, Xiaojiang Yang wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have a question regarding the orientation string gotten from
mri_info. When I apply mri_info command to a DIOM series I generated
programmatically, I get the "???" result, and hence primary slice
direction is also unknown:
......
Orientation : ???
Primary Slice Direction: unknown
......
I already had the " Image Position Patient" and "Image Orientation
Patient" written in the DICOM header. Don't know what other important
info is missing.
Could you tell me what key information is used in DICOM header to
determine this orientation when using mri_info?
Thanks!
John
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