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Dear all,

I am new to Freesurfer, using version 6.0.0.

I am trying to do brain segmentation, using data from two scanners, one called "clinical" and the other called "PRISMA". The clinical scanner uses LPI orientation while the PRISMA one uses RAI. I don't know whether we need to stick to a standard orientation in Freesurfer, so I tested both of them. The result for one volunteer is attached here. In addition to the original images from two scanners, also shown are the PRISMA image flipped to LPI orientation and the clinical image flipped to RAI orientation, using the 3dresample command.

As seen, the volumetry looks similar among all of the four. But if Freesurfer does not require a fixed orientation, then the same image should provide exactly the same volumetry, whether we flip it or not. Am I right? (Question 1) If I understand correctly, there is no statistical variation in the computed volumes, i.e. different runs should give the same volume values.

If Freesurfer does require a fixed orientation in the input image, then how do we know whether the left-right-flipped image is used, as they are roughly symmetric? (Question 2)

Thank you very much!

Ruifeng

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