It uses the geometry information in the input file, so if that is wrong, then the freesurfer output will be wrong. I don't know if BRIKs have this information. If an input file does not have it, FS makes a guess, which might be wrong. It is very strongly encouraged that you use DICOM as input or nifti if you trust how it got to nifit. You are strongly discouraged from using a format that does not preserve this information (like analyze and maybe BRIK).

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:

Hello all,

This is a rather basic question, but I've run into some problems answering it due to the fact that is seems so simple. Much of the data that I have been processing seems to have volumetric asymmetries the opposite of which would be expected, so I was curious as to how freesurfer determines which hemisphere is right and which is left. Does the orientation of the brain matter, or are there labels affixed to each hemisphere in header files? I am using afni .BRIK and .HEAD files. Any help would be appreciated. Thanks,

Nathan

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