MEDx Frequently Asked Questions - Registration
Q: After using motion correction, the top and/or bottom slices of my
images look distorted. Is this normal? Is there some way to avoid this?
If the first and last slice of the functional images includes brain it
possible for the motion correction algorithm to rotate some of the data
out of the volume. This is to be expected if the motion that needs to
be removed involves rotations or z-axis translations.
You can avoid losing data at the top and bottom slices of the volume
is to use the 3D Spatial transformation dialog box to add an extra slice
to the top and bottom of the first time point before calling AIR. This
will cause the registered results to each include an extra slice top and
bottom probably preserving all of the data. To use the 3D Spatial dialog
box to do this you need to:
-
Increase the "Output Size" for Z by 2.
-
Decrease the "Input Center of Transformation" by 0.5.
This should be done to the first time point prior to performing the
motion correction. You should use Nearest Neighbor interpolation since
you are only adding extra slices to the top and bottom and not resampling
the data.
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