Dear Freesurfer Developers,

I have scrutinized the Freesurfer source code from github, found that this might be a bug in Freesurfer.

Basically, the string "Orientation   : ???" comes from the function MRIdircosToOrientationString defined in mri.cpp, which depends on the MRI structure's member ras_good_flag. However, when reading a dicom file using the function DICOMRead2 defined in DICOMRead.cpp, the member ras_good_flag seems to be never been assigned a "ras good flag" value 1. That's why I got the orientation string value of "???".

Would anyone correct or confirm my finding?

Thank you!

John

Xiaojiang Yang Mon, 10 Jan 2022 09:23:09 -0800

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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