Registration of series of 2D images

These programs are mostly tailored for the use of motion compensation in series of myocardial perfusion images and are thought to be used in conjunction with the tools for analyis of image series in the section Tools for Myocardial Perfusion Analysis.

mia-2dgroundtruthreg

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images as decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction a preceding linear registration step is usually required.

mia-2dmany2one-nonrigid

This program registers all images of a conscutively numbered set of images to one common user defined reference.

mia-2dmyoica-full

This program implements the 2D version of the motion compensation algorithm described in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004. The software may first run a linear registration and then a non-linear registration or just one of the both.This version of the program may run all registrations in parallel.

mia-2dmyoica-nonrigid

This program implements the motion compensation algorithm described in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004.

mia-2dmyoica-nonrigid-parallel

This program implements the 2D version of the motion compensation algorithm described in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004.This version of the program may run all registrations in parallel.

mia-2dmyoica-nonrigid2

This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.

mia-2dmyoicapgt

This program implements a two passs motion compensation algorithm. First a linear registration is run based on a variation of Gupta et~al. "Fully automatic registration and segmentation of first-pass myocardial perfusion MR image sequences", Academic Radiology 17, 1375-1385 as described in in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004, followed by a non-linear registration based Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction a preceding linear registration step is usually required. This version of the program may run all registrations in parallel.

mia-2dmyomilles

This program is use to run a modified version of the ICA based registration approach described in Milles et al. 'Fully Automated Motion Correction in First-Pass Myocardial Perfusion MR Image Sequences', Trans. Med. Imaging., 27(11), 1611-1621, 2008. Changes include the extraction of the quasi-periodic movement in free breathingly acquired data sets and the option to run affine or rigid registration instead of the optimization of translations only.

mia-2dmyoperiodic-nonrigid

This program runs the non-rigid registration of an perfusion image series preferable acquired letting the patient breath freely. The registration algorithm implementes G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010

mia-2dmyopgt-nonrigid

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images given as a data set as decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction a preceding linear registration step is usually required.

mia-2dmyoserial-nonrigid

This program runs the non-rigid motion compensation registration of an perfusion image series. The registration is run in a serial manner, this is, only images in temporal succession are registered, and the obtained transformations are applied accumulated to reach full registration. See e.g. Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "A New Similarity Measure for Non-Rigid Breathing Motion Compensation of Myocardial Perfusion MRI ". Proc 30th Annual International IEEE EMBS Conference, pp. 3389-3392. Vancouver, Aug. 2008, doi:10.1109/IEMBS.2008.4649933,

mia-2dmyoset-all2one-nonrigid

This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image.