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##################### # NIFTY_REG PACKAGE # ##################### ############################################################################## -------------------------------- 1 WHAT DOES THE PACKAGE CONTAIN? -------------------------------- The code contains programs to perform rigid, affine and non-linearregistration of 3D images. The rigid and afiine registration are performed using an algorithm presented by Ourselin et al.[1, 2]; whereas the non-rigid registration is based on the work of Modat et al.[3]. Ourselin et al.[1, 2] presented an algorithm called Aladin, which is based on a block-matching approach and a Trimmed Least Square (TLS) scheme. Firstly, the block matching provides a set of corresponding points between a target and a source image. Secondly, using this set of corresponding points, the best rigid or affine transformation is evaluated. This two-step loop is repeated until convergence to the best transformation. In our implementation, we used the normalised cross-correlation between the target and source blocks to extract the best correspondence. The block width is constant and has been set to 4 voxels. A coarse-to-fine approach is used, where the registration is first performed on down-sampled images (using a Gaussian filter to resample images) and finally performed on full resolution images. reg aladin is the name of the command to perform rigid or affine registration. The non-rigid algorithm implementation is based on the Free-From Deformation presented by Rueckert et al.[4]. However, the algorithm has been re-factored in order to speed-up registration. The deformation of the source image is performed using cubic B-splines to generate the deformation field. Concretely, a lattice of equally spaced control points is defined over the target image and moving each point allows to locally modify the mapping to the source image. In order to assess the quality of the warping between both input images, an objective function composed from the Normalised Mutual Information (NMI) and the Bending-Energy (BE) is used. The ob jective function value is optimised using the analytical derivative of both, the NMI and the BE within a conjugate gradient scheme. reg f3d is the command to perform non-linear registration. A third program, called reg resample, is been embedded in the package. It uses the output of reg aladin and reg f3d to apply transformation, generate deformation fields or Jacobian map images for example. The code has been implemented for CPU and GPU architecture. The former code is based on the C/C++ language, whereas the later is based on CUDA (http://www.nvidia.com). The nifti library (http://nifti.nimh.nih.gov/) is used to read and write images. The code is thus dealing with nifti and analyse formats. If you are planning to use any of our research, we would be grateful if you would be kind enough to cite reference(s) 1, 2 (rigid or affine) and/or 3 (non-rigid). ############################################################################## ----------------------- 2 HOW TO BUILD THE CODE ----------------------- The code can be easily build using cmake (http://www.cmake.org/). The latest version can be downloaded from http://www.cmake.org/cmake/resources/software.html Assuming that the code source are in the source path folder, you will have to first create a new folder, i.e. build path (#1) and then to change directory to move into that folder (#2). #1 >> mkdir build path #2 >> cd build path There you will need to call ccmake (#3a) in order to fill in the build options. If you don’t want to specify options, we could just use cmake (#3b) and the default build values will be used. #3a >> ccmake source path #3b >> cmake source path The main option in the ccmake gui are defined bellow: >BUILD ALADIN if this flag is set to ON, the reg aladin command will be created >BUILD F3D if this flag is set to ON, the reg f3d command will be created >BUILD RESAMPLE if this flag is set to ON, the reg resample command will be created >CMAKE BUILD INSTALL options are Release, RelWithDebInfo or Debug >USE CUDA if the flag is set to ON, both version CPU and GPU version can be used; otherwise, only the CPU version is compiled >USE DEBUG if the flag is set to ON, the program will print out some information which are only used to debug >USE SSE if the flag is set to ON, the spline computation will be perform using sse in order to speed-up to processing If the USE CUDA flag is ON, some other informations will be require to use the Cuda compiler. The flag CUDA TOOL ROOT DIR expect the path to the cuda installation (/usr/local/cuda for example) and the CUDA TOOLKIT ROOT DIR expected the path the cuda SDK installation (/usr/local/cuda-sdk/C for example). Once all the flags are properly filled in, just press the ”c” to configure the Make- file and then the ”g” key to generate them. In the prompt, you just have to make (#4) first and then make install (#5). #4 >> make #5 >> make install ############################################################################## --------- 3 EXAMPLE --------- In this example, we will register two nifti images called target img.nii and source img.nii. Firstly, we perform an affine registration using reg aladin using the following command line: # reg aladin -target target img.nii -source source img.nii ... -aff source-to-target_affine.txt More options can be specified, for more details, use the command: # reg aladin -help Secondly, we will perform a non-rigid registration between the two previous images and the warping will be initialised by the previously found affine transformation: # reg f3d -target target img.nii -source source img.nii ... -aff source-to-target_affine.txt -cpp source-to-target cpp.nii ... -result source-to-target warped.nii As previously, more details can be found using the command: # reg f3d -help Lastly, the control point position image will be used to generate the Jacobian map of the transformation. This will be done using: # reg resample -target target img.nii -source source img.nii ... -cpp source-to-target cpp.nii -jac source-to-target jac.nii Once again, the ”-help” argument gives more details about the options. Please note that the affine matrix does not need to be specified. We choose to include the affine transformation in the control point position image. ############################################################################## --------- 4 LICENSE --------- Copyright (c) 2009, University College London, United-Kingdom All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of the University College London nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ############################################################################## --------- 5 CONTACT --------- For any comment, please, feel free to contact Marc Modat (m.modat@ucl.ac.uk). ############################################################################## ------------ 6 REFERENCES ------------ [1] Sebastien Ourselin, A Roche, G Subsol, Xavier Pennec, and Nicholas Ayache. Reconstructing a 3d structure from serial histological sections. Image and Vision Computing, 19(1-2):25–31, 2001. [2] Robust registration of multi-modal images: Towards real-time clinical applications, 2002. [3] Marc Modat, Gerard G Ridgway, Zeike A Taylor, Manja Lehmann, Josephine Barnes, Nick C Fox, David J Hawkes, and S´ebastien Ourselin. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio, accepted. [4] D. Rueckert, L.I. Sonoda, C. Hayes, D.L.G. Hill, M.O. Leach, and D.J. Hawkes. Nonrigid Registration Using Free-Form Deformations: Application to Breast MR Images. IEEE Trans. Med. Imag., 18:712–721, 1999. ############################################################################## ############################################################################## ############################################################################## ##############################################################################