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:
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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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