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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.
[image: image.png]
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