Directional Cosines in Anatomist

Questions about Anatomist manipulation

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Directional Cosines in Anatomist

Post by ericbarnhill »


I am wondering if Anatomist uses the directional cosine information when it loads brains. In one project have lots of sagittal scans with orientation 0\1\0\0\0\-1 and they come into anatomist with a saggital view when I choose axial window. Of course when I set the AC/PC for the pipeline it both flips and rotates the brain, but I am struggling to figure out whether to describe a brain with this orientation matrix as radiological or neurological. Thanks for any help.

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Re: Directional Cosines in Anatomist

Post by riviere »

Hi Eric,

Well, it depends on the input file format...
The NIFTI reader implements it, and relies on the scanner coords rotation quaternion to determine the orientation of the image, and apply the required flips.
But the DICOM reader does not, currently. Orientations specified in DICOM files are not interpreted by Anatomist. We're not very good at Dicom reading...
The best option if you are using Dicom files is to convert them to Nifti using a program which will correctly read and set the orientation and transformation information. You can try mriconvert, or dcm2nii (part of Mricron) for instance.
Once correctly converted to NIFTI, orientation should be OK.

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