3dQwarp (the engine inside our nonlinear warping scripts) also has two options that let you give extra weight to registration in a particular small region. From the -help output of 3dQwarp:
-wball x y z r f =
Enhance automatic weight from '-useweight' by a factor
of 1+f*Gaussian(FWHM=r) centered in the base image at
DICOM coordinates (x,y,z) and with radius 'r'. The
goal of this option is to try and make the alignment
better in a specific part of the brain.
* Example: -wball 0 14 6 30 40
to emphasize the thalamic area (in MNI/Talairach space).
* The 'r' parameter must be positive (in mm)!
* The 'f' parameter must be between 1 and 100 (inclusive).
* '-wball' does nothing if you input your own weight
with the '-weight' option :(
* '-wball' does change the binary weight created by
the '-noweight' option.
* You can only use '-wball' once in a run of 3dQwarp.
*** The effect of '-wball' is not dramatic. The example
above makes the average brain image across a collection
of subjects a little sharper in the thalamic area, which
might have some small value. If you care enough about
alignment to use '-wball', then you should examine the
results from 3dQwarp for each subject, to see if the
alignments are good enough for your purposes.
-wmask ws f = Similar to '-wball', but here, you provide a dataset 'ws'
that indicates where to increase the weight.
* The 'ws' dataset must be on the same 3D grid as the base
dataset.
* 'ws' is treated as a mask -- it only matters where it
is nonzero -- otherwise, the values inside are not used.
* After 'ws' comes the factor 'f' by which to increase the
automatically computed weight. Where 'ws' is nonzero,
the weighting will be multiplied by (1+f).
* As with '-wball', the factor 'f' should be between 1 and 100.
* You cannot use '-wball' and '-wmask' together!
If the region defined by -wball or -wmask is small (the usual case), the factor 'f' should be large-ish -- 40 or more -- otherwise the effect will not be noticeable. In my experiments with the human thalamus, the effects were small in any case, but visible.
