Abstract
We present an information-theoretic approach to the registration of images with directional information, especially for diffusion-weighted images (DWIs), with explicit optimization over the directional scale. We call it locally orderless registration with directions (LORDs). We focus on normalized mutual information as a robust information-theoretic similarity measure for DWI. The framework is an extension of the LOR-DWI density-based hierarchical scale-space model that varies and optimizes the integration, spatial, directional and intensity scales. As affine transformations are insufficient for inter-subject registration, we extend the model to nonrigid deformations. We illustrate that the proposed model deforms orientation distribution functions (ODFs) correctly and is capable of handling the classic complex challenges in DWI registrations, such as the registration of fiber crossings along with kissing, fanning, and interleaving fibers. Our experimental results clearly illustrate a novel promising regularizing effect, which comes from the nonlinear orientation-based cost function. We show the properties of the different image scales, and we show that including orientational information in our model makes the model better at retrieving deformations in contrast to standard scalar-based registration.
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Contact us or henrikgjensen@gmail.com for the code or examples.
References
Abramowitz, M., Stegun, I.: Handbook of Mathematical Functions, With Formulas, Graphs, and Mathematical Tables. Dover, New York (1974)
Avants, B.B., Tustison, N., Song, G.: Advanced normalization tools (ants). Insight j 2, 1–35 (2009)
Bishop, C.M.: Pattern Recognition and Machine Learning. Springer, Berlin (2006)
Darkner, S., Sporring, J.: Generalized partial volume: an inferior density estimator to parzen windows for normalized mutual information. In: IPMI, LNCS, vol. 6801, pp. 436–447. Springer, Berlin (2011)
Darkner, S., Sporring, J.: Locally orderless registration. IEEE Trans. Pattern Anal. Mach. Intell. 35(6), 1437–1450 (2013)
Darkner, S., Pai, A., Liptrot, M., Sporring, J.: Collocation for diffeomorphic deformations in medical image registration. IEEE Trans. Pattern Anal. Mach. Intell. 40(7), 1570–1583 (2018). https://doi.org/10.1109/TPAMI.2017.2730205
Descoteaux, M., Angelino, E., Fitzgibbons, S., Deriche, R.: Regularized, fast, and robust analytical q-ball imaging. Magn. Reson. Med. 58(3), 497–510 (2007)
Fischl, B.: Freesurfer. Neuroimage 62(2), 774–781 (2012)
Gallier, J., Quaintance, J.: Differential Geometry and Lie Groups. A second course, Geometry and Computing, vol. 13. Springer, Berlin (2020)
Garyfallidis, E., Brett, M., Amirbekian, B., Rokem, A., Van Der Walt, S., Descoteaux, M., Nimmo-Smith, I.: Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinform. 8, 8 (2014)
Helmholtz, H.: Uber integrale der hydrodynamischen gleichungen, welcher der wirbelbewegungen entsprechen’’ (on integrals of the hydrodynamic equations which correspond to vortex motions). Journal für die reine und angewandte Mathematik 55(8), 25–55 (1858)
Hermosillo, G., Chefd’Hotel, C., Faugeras, O.: Variational methods for multimodal image matching. Int. J. Comput. Vis. 50(3), 329–343 (2002)
Irfanoglu, M.O., Nayak, A., Jenkins, J., Hutchinson, E.B., Sadeghi, N., Thomas, C.P., Pierpaoli, C.: Dr-tamas: diffeomorphic registration for tensor accurate alignment of anatomical structures. Neuroimage 132, 439–454 (2016)
Jenkinson, M., Beckmann, C.F., Behrens, T.E., Woolrich, M.W., Smith, S.M.: Fsl. Neuroimage 62(2), 782–790 (2012)
Jensen, H.G., Lauze, F., Nielsen, M., Darkner, S.: Locally orderless registration for diffusion weighted images. In: International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 305–312. Springer, Berlin (2015)
Johansen-Berg, H., Behrens, T.E.: Diffusion MRI: From Quantitative Measurement to In Vivo Neuroanatomy. Academic Press, London (2013)
Jupp, P., Mardia, K.: A unified view of the theory of directional statistics, 1975–1988. Int. Stat. Rev./Revue Internationale de Statistique 261–294 (1989)
Klein, S., Staring, M., Murphy, K., Viergever, M.A., Pluim, J.P.: Elastix: a toolbox for intensity-based medical image registration. IEEE Trans. Med. Imaging 29(1), 196–205 (2010)
Koenderink, J.J., Van Doorn, A.J.: The structure of locally orderless images. Int. J. Comput. Vis. 31(2), 159–168 (1999)
O’Donnell, L.J., Daducci, A., Wassermann, D., Lenglet, C.: Advances in computational and statistical diffusion MRI. NMR in Biomedicine (2017)
Riyahi-Alam, S., Peroni, M., Baroni, G., Riboldi, M.: Regularization in deformable registration of biomedical images based on divergence and curl operators. Methods Inf. Med. 53(01), 21–28 (2014)
Rueckert, D., Aljabar, P., Heckemann, R.A., Hajnal, J.V., Hammers, A.: Diffeomorphic registration using b-splines. In: International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 702–709. Springer, Berlin (2006)
Rueckert, D., Sonoda, L.I., Hayes, C., Hill, D.L., Leach, M.O., Hawkes, D.J.: Nonrigid registration using free-form deformations: application to breast MR images. IEEE Trans. Med. Imaging 18(8), 712–721 (1999)
Schmidt, M.: minfunc: unconstrained differentiable multivariate optimization in matlab. Software available at https://www.cs.ubc.ca/~schmidtm/Software/minFunc.html (2005)
Semechko, A.: Suite of functions to perform uniform sampling of a sphere. Software available at https://www.mathworks.com/matlabcentral/fileexchange/37004-suite-of-functions-to-perform-uniform-sampling-of-a-sphere (2012). Accessed 2017
Sporring, J., Darkner, S.: Jacobians for Lebesgue registration for a range of similarity measures. Department of Computer Science, University of Copenhagen, Tech. Rep 4 (2011)
Sra, S., Karp, D.: The multivariate Watson distribution: maximum-likelihood estimation and other aspects. J. Multivar. Anal. 114, 256–269 (2013)
Studholme, C., Hill, D.L., Hawkes, D.J.: An overlap invariant entropy measure of 3d medical image alignment. Pattern Recogn. 32(1), 71–86 (1999)
Tao, X., Miller, J.V.: A method for registering diffusion weighted magnetic resonance images. In: Medical Image Computing and Computer-Assisted Intervention—MICCAI 2006, pp. 594–602. Springer, Berlin (2006)
Tournier, J., Calamante, F., Connelly, A., et al.: Mrtrix: diffusion tractography in crossing fiber regions. Int. J. Imaging Syst. Technol. 22(1), 53–66 (2012)
Treiber, J.M., White, N.S., Steed, T.C., Bartsch, H., Holland, D., Farid, N., McDonald, C.R., Carter, B.S., Dale, A.M., Chen, C.C.: Characterization and correction of geometric distortions in 814 diffusion weighted images. PLoS ONE 11(3), e0152472 (2016)
Van Essen, D.C., Smith, S.M., Barch, D.M., Behrens, T.E., Yacoub, E., Ugurbil, K., Consortium, W.M.H., et al.: The WU-Minn human connectome project: an overview. Neuroimage 80, 62–79 (2013)
Van Hecke, W., Leemans, A., D’Agostino, E., De Backer, S., Vandervliet, E., Parizel, P.M., Sijbers, J.: Nonrigid coregistration of diffusion tensor images using a viscous fluid model and mutual information. IEEE Trans. Med. Imaging 26(11), 1598–1612 (2007)
Wang, Y., Gupta, A., Liu, Z., Zhang, H., Escolar, M.L., Gilmore, J.H., Gouttard, S., Fillard, P., Maltbie, E., Gerig, G., et al.: DTI registration in atlas based fiber analysis of infantile Krabbe disease. Neuroimage 55(4), 1577–1586 (2011)
Wang, Y., Yu, Q., Liu, Z., Lei, T., Guo, Z., Qi, M., Fan, Y.: Evaluation on diffusion tensor image registration algorithms. Multimed. Tools Appl. 75(13), 8105–8122 (2016)
Wang, Y., Shen, Y., Liu, D., Li, G., Guo, Z., Fan, Y., Niu, Y.: Evaluations of diffusion tensor image registration based on fiber tractography. Biomed. Eng. Online 16(1), 9 (2017)
Wells, W., Viola, P., Atsumi, H., Nakajima, S., Kikinis, R.: Multi-modal volume registration by maximization of mutual information. Med. Image Anal. 1(1), 35–51 (1996)
Yeo, B.T., Vercauteren, T., Fillard, P., Peyrat, J.M., Pennec, X., Golland, P., Ayache, N., Clatz, O.: DT-REFinD: diffusion tensor registration with exact finite-strain differential. IEEE Trans. Med. Imaging 28(12), 1914–1928 (2009)
Zhang, H., Yushkevich, P.A., Alexander, D.C., Gee, J.C.: Deformable registration of diffusion tensor MR images with explicit orientation optimization. Med. Image Anal. 10(5), 764–785 (2006)
Zhang, P., Niethammer, M., Shen, D., Yap, P.T.: Large deformation diffeomorphic registration of diffusion-weighted imaging data. Med. Image Anal. 18(8), 1290–1298 (2014)
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This research was supported by Center for Stochastic Geometry and Advanced Bioimaging, funded by grant 8721 from the Villum Foundation.
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Jensen, H.G., Lauze, F. & Darkner, S. Information-Theoretic Registration with Explicit Reorientation of Diffusion-Weighted Images. J Math Imaging Vis 64, 1–16 (2022). https://doi.org/10.1007/s10851-021-01050-2
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DOI: https://doi.org/10.1007/s10851-021-01050-2