B-spline Grid, Image and Point based Registration

Solved Bugs in diffeomorphic functions. Tested in Ubuntu and with LCC compiler

Added MakeDiffeomorphic for deformations without folding. New clean multi-threading c-code.

Fixed Nan in SSD calculation. Added numerical b-spline inverse. Added bi-cubic code

Major Update! Improved / fixed bugs in "Mutual information", new affine weighting par. in 3D. Fixed bug, which caused the error to decrease after refining a few times to a very fine b-spline grid. Added Point Registration examples.

Added Corresponding Point based registration of Lee. Merged 2D and 3D registration functions into one file. Replaced for-loops by faster 1D index operations.

Added manually_warp_images function. Now uses localized mutual information for the error calculation, not only for the gradient of the error. Split register_images and register_volumes in sub-functions.

Fixes for Linux Compiler

Fixed bug, 3D registration empty Fx and Fz matrix.

Fix Gaussian filter function

Fixed Single cubic interpolation bug, and addpaths.m in low_level_examples

Solved mask bug reported by siamak yousefi.
Also changed default smoothness penalty from 0.001 to 0.01 , which is probably better for most applications.

Major code speed up by look up tables and separate SDD code. Also some bug Fixes in Mask code...

Major bug z-dimension fixed in volume registration

Bug fixed in index 3D cubic interpolation, resulted in zero resulting volumes

Minor bug, Mask is now resized to fit size Istatic (if not already).

Added Cubic interpolation!, fixed bug and comment in masks mutual information, interpolation now in separate file c. file

example 3d nonrigid fixed

Bug LCC compiler doesn't link floorf fixed. Also fixed NaN bug in image_difference.m

Tri Ngo provided me with Linux multi-threaded code, which I added, thus the registration now supports multi-threaded Windows, Linux and (Mac Os)?
Also fixed last ; bug ...

";" removed to fix a boundary bug

Speed up affine 3D registration (2x), and some other small improvements.

Added 2D RGB image support

Landmarks can now be used as transformation regularization.

Fixed out of bounds bug, reported by D.C. Karhoff

Bug fixed in image dimensions in backwards2forward c-code and updated movepixels files to allow pixels outside image to be zero or nearest value inside image.

Changed parameter "size of region influenced by a control point" in final refinement step. Resulting in a speed up of 150% in gradient calculation in this last step.

Fixed a bug: The moving grid was used to determine the region influenced by a control point in gradient registration, this is changed in a uniform static grid. (b-splines are always determined on a uniform grid).

Multi-threaded registration now uses the number of threads set by maxNumCompThreads. New Quasi newton optimizer fminlbfgs. Speed ups in the smoothness penalty, and some other files.

Single Threaded files are updated to all code in the Multiple Threaded files, and tested...

2D available in 100% Matlab code. Eulerian strain images available. Parts of images can be masked. Forward transformation field now also available.

Bug fixed: The rigid transformation optimizers crashed with images with strange dimensions

Added registration smoothness penalty.