Hi,

I am trying to realign FA-maps of one subject, who was scanned at two different time points. After running BET I am using FLIRT for realigning (rigid body transform, 6D OF) the B0 images (extracted from the DTI data set) of the second measurement to the B0 images of the first measurement and as secondary images to apply the transform to I take the FA maps of the second measurement.

The realignment works fine, but  the FA-map of the second measuresment (the realigned one) was "smoothed" during the process. Since the first FA-map was not processed, the two maps differ in terms of their "resolution / smootheness".

Is there a way either to turn off the "smoothing" during the realignment or to smoothe the first FA-map (which was not transformed) in a similar way? (I do not want to realign all images to a "standard brain" due to gross pathology)

Any help is appreciated,

Yours , Oliver