ENH:  Working point set registration, finally.  Need to update with this ITK patch a6b3426842261996350b261cf0c603623ced7484
Add option -y 0 to remove rigid components of the average affine transform when updating the template.

Made -y 1 the default for backwards compatibility with template construction scripts.

Hard coded -y 0 into antsLongitudinalCorticalThickness.sh. Because the number of images in this template construction call is small, the average translation / rotation can be substantial and this can cause the template to be rotated or shifted out of the field of view.

Also in antsLongitudinalCorticalThickness.sh, added a 5 voxel pad to the SST. If the top of the brain is cut off, or if there are varying amounts of spine / neck at the bottom of the images, padding the fixed image can improve affine alignment.
ENH: Update ITK for FixedParameter setting

ITK now preserves the fixed parameters (i.e. the center of rotation
for MatrixOffsetBase) objects during the inversion process.  This is important
so that the parameters of Inv(Inv(T)) ~= the parameters of T.  It is also
important if you desire to optimize the the inverse transform from the moving
image to the fixed image.
Merge pull request #121 from BRAINSia/FixedParametersITK

ENH: Update ITK for FixedParameter setting
COMP: Remove compiler warning.
Merge pull request #122 from stnava/templateShapeUpdateNoRigid

Add option -y 0 to remove rigid components of the average affine transfo...
ENH:  Update ITK superbuild for point set registration.
Merge pull request #123 from stnava/PointSetRegBeginnings

ENH:  Working point set registration, finally.  Need to update with this...
ENH: Write collapsed output composite transform

The collapsed output composite transform was not
being written to disk, even when requested.
ENH: Initialize linear transforms with the output of previous stage
ENH: Change the auto initialization transform to a rigid transform
ENH: Add the linear transforms direct initialization flag to command line

A new command line, called "initialize-linear-transforms-per-stage", is
added that allows the direct initialization of the current linear stage
transform from the previous stage's linear transform; this allows
multiple linear stages to be run where each stage directly updates the
estimated linear transform from the previous stage.
(e.g. Translation -> Rigid -> Affine).
ENH: Make the collapsed transform keep the center of rotation

Previously the collapsed linear affine transform had fixed parameters
as all zero. Now we find the last transform that has a center, and set
that as the fixed parameters of the total transform, and it is done only
once.
If you wish to set the center explicitly, set before Offset computations
are done.  To define an affine transform, you must set the matrix, center,
and translation OR the matrix and offset
Merge pull request #124 from BRAINSia/CompositeTransformFixedParameterFixes

Composite transform fixed parameter fixes
ENH: more graceful handling of low intensity variation timepoints
BUG:  Do not output h5 files unless specified '-a 1'
BUG:  Output composite non-collapsed transform given the proper flags.
ENH: direct initialization for SyN
ENH: Change the direct initialization flag name

Since the direct initialization is added for SyN in addition to the
linear transforms, the "initialize-linear-transforms-per-stage" flag
name is changed to the "initialize-transforms-per-stage".
WIP: write syn composite