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Understanding the World Coordinates

Questions or comments about Mango, webMango, iMango or Papaya.

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Understanding the World Coordinates

Postby mkaptan » Fri Mar 29, 2019 12:09 pm

Dear experts,

Firstly, thanks for this really nice tool!
I just started using Mango so I have a rather naive question, sorry about that.
I have an MRI image with 24 axial slices. When I switched to the world coordinates the centre slice of the image( z = 0 )does not correspond to my middle slice in scanner coordinates but rather somewhere like the 18th slice. Does that mean it I have a problem regarding the image acquisition?

Thanks a lot,
Kind Regards,
Merve
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Re: Understanding the World Coordinates

Postby admin » Sun Apr 14, 2019 3:48 pm

Hi. Sorry for the late reply. I'm not sure if these are NIFTI or DICOM images that you have.

In NIFTI images, the origin is stored in the header and whatever software generated the NIFTI image would determine what the origin value is. The world coordinates are intended to be used with images that have been aligned to a standard space, such as Talairach or MNI. In these cases, the origin would be aligned to some part of the anatomy and not necessarily the center slice.

These "world coordinates" are less applicable to DICOM data, at least currently in Mango. I believe for DICOM data, it picks the center of the image volume as the "origin".
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