The orientation itself does not matter in terms of running FS on an individual. However, I would be very careful about doing a statistical analysis where some subjects are axial and some are saggital as the change in the phase encode direction can cause bias. At the very least, any comparisons should be balanced (ie, same number of axials in each group, same number of saggitals, ...)

doug

David Qixiang Chen wrote:

Hi all, Just wondering if the scan orientation for input DICOMs matter. I know that Analyze format does not preserve left/right orientation information, but would a saggital DICOM scan have the same problem? We have a lot of axial scans, would incorporating freesurfer subjects with saggital scans in our comparisons cause any problems? Assuming that the slice thickness is 1mm with 0 spacing at 3T, with 256x256 res. We are using GE Signa HDx scanners.

Thanks

• David Qixiang Chen

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