Initial commit of revised version of FRAT.
Will include better 2D/3D support and a more object-oriented and modular approach to LDDMM registration and atlas building.
Running version of the new datastructures. Next step, implement advection equations.
Added numerics classes to support generic advection. As well as a semi Lagrangian specialization. Still requires a new version of VectorImageUtils. Will not compile at this stage.
Added utility functions. Need testing to see if they compile and work right.
Fixed syntax errors in the utility functions. Need to add tests for all of them.
Added a base class for image management, which should be useful for later time-series processing.
Converted more utility functions. Added single scale image manager. Added DTIProcess as external library. Compiles, but is currently untested.
First working version of line search with scalar example. Next step, implementation of actual algorithms.
Added the initial stages of a spatiotemporal state class.
Non-working version. Pure backup. Needs to be finished and fixed, so that it compiles and runs.
Code reorganization and seems to compile. Finish LDDMM and start debugging.
Fixed some compilation issues, added some convenience functions to free memory. Still not tested.
Cleaned up LDDMM code a bit. Still not tested, but almost fully implemented now.
Fixed various const-correctness issues. Now has a full LDDMM implementation, which compiles, but has not been tested yet (so likely has many bugs still).
Some bugfixes for the intialization of velocity fields and computation of the time step. Still not running.
Fixed a couple of bugs. Still not working. Next check adjoint and gradient computation.
Need to fix the kernel. Otherwise weird things will happen to the memory.
Fixed a number of bugs in the line search and the FFT. Seems to almost work now. Need to test still, especially with blurred images.
Fixed issues with LDDMM. Registration seems to work for appropriate spacings of the image (as in I0_short.nhdr and I1_short.nhdr). However, result is not exactly the same as for the matlab code. Need to investigate why. Also, need to make the parameter settings for the kernel useful for real applications and spacings.
Still searching the bug that makes the velocity energies slightly different. This commit contains some debug statements to help track it down.