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Avoiding asymmetry-induced bias in longitudinal image processing

Martin Reuter, Bruce Fischl
2011 NeuroImage  
Longitudinal image processing procedures frequently transfer or pool information across time within subject, with the dual goals of reducing the variability and increasing the accuracy of the derived measures  ...  In order to reduce variability and detect true change in structure or function, it is important to be able to transfer and share information across time.  ...  Biased registration (lack of inverse consistency) In order to study differences across time within the same subject, images are frequently registered using either a rigid or affine registration or higher  ... 
doi:10.1016/j.neuroimage.2011.02.076 pmid:21376812 pmcid:PMC3260043 fatcat:2uveduwnqfdahcr72bkq3sbs6u

Multi-Contrast Computed Tomography Healthy Kidney Atlas [article]

Ho Hin Lee, Yucheng Tang, Kaiwen Xu, Shunxing Bao, Agnes B. Fogo, Raymond Harris, Mark P. de Caestecker, Mattias Heinrich, Jeffrey M. Spraggins, Yuankai Huo, Bennett A. Landman
2020 arXiv   pre-print
Briefly, we introduce a deep learning-based volume of interest extraction method and an automated two-stage hierarchal registration pipeline to register abdominal volumes to a high-resolution CT atlas  ...  The identified datasets used for the analysis described were obtained from the Research Derivative (RD), database of clinical and related data.  ...  This study was in part using the resources of the Advanced Computing Center for Research and Education (ACCRE) at Vanderbilt University, Nashville, TN.  ... 
arXiv:2012.12432v2 fatcat:q24uyoiaavbydlznmfxpwaw4dm

Towards respiration management in radiation treatment of lung tumors: Transferring regions of interest from planning CT to kilovoltage X-ray images

E Ataer-Cansizoglu, E Bas, M A Yousuf, Sheng You, W D D'Souza, D Erdogmus
2010 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology  
Our approach gives accurate results for rigid registration and provides a starting point to track tumors using the X-ray images during the treatment.  ...  Our approach generates Digitally Reconstructed Radiographs (DRRs) using bilateral filter smoothing and computes rigid registration with kV images since the position and orientation of patient might differ  ...  The parameters of the rigid registration (R, t) are selected such that the inner product between the density functions ζ 1 (x) and ζ 2 (f (x)) is maximized, where ζ 1 and ζ 2 are the KDE estimates of a  ... 
doi:10.1109/iembs.2010.5626126 pmid:21095744 fatcat:mv6cpqinqbg3jg2owbzfi6h3h4

Alignment of Tractography Streamlines using Deformation Transfer via Parallel Transport [article]

Andrew Lizarraga, David Lee, Antoni Kubicki, Ashish Sahib, Elvis Nunez, Katherine Narr, Shantanu H. Joshi
2021 arXiv   pre-print
We present a novel deformation metric between tracts that allows one to compare tracts while simultaneously obtaining a registration.  ...  Another approach by O'Donnell et al. has used distributions of fibers for unbiased group registration of tractography representations [13] .  ...  registration over rigid alignment.  ... 
arXiv:2108.03697v1 fatcat:nie2dqmce5gwxgplxgzshzlmce

Framework for integrated MRI average of the spinal cord white and gray matter: The MNI–Poly–AMU template

V.S. Fonov, A. Le Troter, M. Taso, B. De Leener, G. Lévêque, M. Benhamou, M. Sdika, H. Benali, P.-F. Pradat, D.L. Collins, V. Callot, J. Cohen-Adad
2014 NeuroImage  
The template was created by co-registering T 2 -weighted images (N=16 healthy volunteers) using a series of pre-processing steps followed by non-linear registration.  ...  ) and unbiased extraction of multi-parametric data.  ...  These segmented structures can be used as ROIs for multiparametric MRI techniques (e.g., diffusion imaging, magnetization transfer, functional MRI).  ... 
doi:10.1016/j.neuroimage.2014.08.057 pmid:25204864 fatcat:lquuachaybffdbzfxsjo5povgq

Unbiased diffeomorphic atlas construction for computational anatomy

S. Joshi, Brad Davis, Matthieu Jomier, Guido Gerig
2004 NeuroImage  
and object segmentation via registration of anatomical labels.  ...  Large sets of images are mapped into a common coordinate system to study intra-population variability and inter-population differences, to provide voxel-wise mapping of functional sites, and help tissue  ...  This supports use of deformable atlas registration where constraints are provided by a volumetric, unbiased atlas.  ... 
doi:10.1016/j.neuroimage.2004.07.068 pmid:15501084 fatcat:q4uftrvdnfdkbdkgucvegac6ku

A Motion Correction Strategy for Multi-Contrast based 3D parametric imaging: Application to Inhomogeneous Magnetization Transfer (ihMT) [article]

Lucas Soustelle, Julien Lamy, Arnaud Le Troter, Andreea Hertanu, Maxime Guye, Jean-Philippe Ranjeva, Gopal Varma, David C. Alsop, Jean Pelletier, Olivier Girard, Guillaume Duhamel
2020 bioRxiv   pre-print
The proposed method was compared to Motion Correction with FMRIB's Linear Image Registration Tool (MCFLIRT) function in FSL over 13 subjects.  ...  Methods A framework for motion correction, including image pre-processing enhancement and rigid registration to an iteratively improved target image, was developed.  ...  Diffusion Tensor Imaging, Magnetization Transfer) and functional (e.g. Arterial Spin Labeling) evaluations.  ... 
doi:10.1101/2020.09.11.292649 fatcat:shooargvv5acfiuqn3csa4nhby

Within-subject template estimation for unbiased longitudinal image analysis

Martin Reuter, Nicholas J. Schmansky, H. Diana Rosas, Bruce Fischl
2012 NeuroImage  
In this paper we introduce a novel longitudinal image processing framework, based on unbiased, robust, withinsubject template creation, for automatic surface reconstruction and segmentation of brain MRI  ...  Then use the rigid transforms to initialize an iterative affine registration employing the intensity normalized full head images. 3.  ...  Fine tune those affine registrations by using the affine maps to initialize a final set of registrations of the skull stripped brain images to the template, where only rigid parameters are allowed to change  ... 
doi:10.1016/j.neuroimage.2012.02.084 pmid:22430496 pmcid:PMC3389460 fatcat:gv4muaiizvfsxizgqkoi6ixupm

Automatic brain segmentation in rhesus monkeys

Martin Styner, Rebecca Knickmeyer, Sarang Joshi, Christopher Coe, Sarah J. Short, John Gilmore, Josien P. W. Pluim, Joseph M. Reinhardt
2007 Medical Imaging 2007: Image Processing  
We determine the atlas from training images by iterative, joint deformable registration into an unbiased average image. On this atlas, probabilistic tissue maps and a lobar parcellation.  ...  Other regional definitions on the atlas can also straightforwardly be used as segmentation.  ...  These right hemispheric definitions were mirrored at the midsagittal plane using a simple axial flip operation followed by rigid registration to produce the initial left hemispheric lobar parcellation.  ... 
doi:10.1117/12.710027 dblp:conf/miip/StynerKJCSG07 fatcat:3seeld5rl5c5xkofy4tu7uo5fu

Comprehensive ultrahigh resolution whole brain in vivo MRI dataset as a human phantom

Falk Lüsebrink, Hendrik Mattern, Renat Yakupov, Julio Acosta-Cabronero, Mohammad Ashtarayeh, Steffen Oeltze-Jafra, Oliver Speck
2021 Scientific Data  
reconstruction, 330 µm quantitative susceptibility mapping, up to 450 µm structural T2-weighted imaging, 700 µm T1-weighted back-to-back scans, 800 µm diffusion tensor imaging, one hour continuous resting-state functional  ...  However, before doing so, the different directions were motion corrected by rigid registration of the time series data to an unbiased template.  ...  In a multistage rigid registration approach, an average volume from all directions was created and then each direction was registered to this unbiased average.  ... 
doi:10.1038/s41597-021-00923-w pmid:34035308 fatcat:xa7ojefsvvgknjodkct3swzne4

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain

Sergey Osechinskiy, Frithjof Kruggel
2011 Anatomy Research International  
Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions.  ...  functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines.  ...  All cases used CC cost function and TPS (N/A to rigid case), except for CG, which is implemented only for SSD and B-Splines.  ... 
doi:10.1155/2011/287860 pmid:22567290 pmcid:PMC3335496 fatcat:qdwyg6fczzhsxnw4iiqdf7pjri

Front Matter: Volume 10574

Proceedings of SPIE, Elsa D. Angelini, Bennett A. Landman
2018 Medical Imaging 2018: Image Processing  
using a Base 36 numbering system employing both numerals and letters.  ...  SPIE uses a seven-digit CID article numbering system structured as follows:  The first five digits correspond to the SPIE volume number.  The last two digits indicate publication order within the volume  ...  10574 06 Constructing statistically unbiased cortical surface templates using feature-space covariance SESSION 2 DEEP LEARNING: SEGMENTATION 07 Segmentation of anatomical structures in cardiac CTA using  ... 
doi:10.1117/12.2315755 fatcat:jdfbaent6vhu5dwlrqrqt66vce

Image registration of ex-vivo MRI to sparsely sectioned histology of hippocampal and neocortical temporal lobe specimens

Maged Goubran, Cathie Crukley, Sandrine de Ribaupierre, Terence M. Peters, Ali R. Khan
2013 NeuroImage  
registration with the ex-vivo MRI.  ...  We evaluated our registration method on specimens resected from patients undergoing anterior temporal lobectomy (N=7) and found our method to have a mean target registration error of 0.76 ± 0.66 and 0.98  ...  We used a fast non-rigid registration that makes use of a B-spline deformation field and a normalized mutual information cost-function (Rueckert et al., 1999; Modat et al., 2010) (NiftyReg,  ... 
doi:10.1016/j.neuroimage.2013.07.053 pmid:23891884 fatcat:hlndu6kf2zdftijcarvv4yyxde

Performance Evaluation of Grid-Enabled Registration Algorithms Using Bronze-Standards [chapter]

Tristan Glatard, Xavier Pennec, Johan Montagnat
2006 Lecture Notes in Computer Science  
We computed the accuracy of 4 different rigid registration algorithms on longitudinal MRI images of brain tumors. Results showed an average subvoxel accuracy of 0.4 mm and 0.15 degrees in rotation.  ...  Performance Evaluation Using Bronze Standards The accuracy performances of registration algorithms are critical for many clinical procedures but quantifying them is difficult due to the lack of gold standard  ...  A complete system would include an ontology of registration problems (modalities, anatomical region, rigid or non-rigid registration, etc), of registration algorithms (input/output data types, method used  ... 
doi:10.1007/11866763_19 fatcat:6jtwbikqengnha6edy5mzkje54

On Removing Interpolation and Resampling Artifacts in Rigid Image Registration

I. Aganj, B. T. T. Yeo, M. R. Sabuncu, B. Fischl
2013 IEEE Transactions on Image Processing  
These artifacts negatively affect the accuracy of registration by producing local optima, altering the gradient, shifting the global optimum, and making rigid registration asymmetric.  ...  We show that image registration using conventional interpolation and summation approximations of continuous integrals can generally fail because of resampling artifacts.  ...  They showed that these artifacts disappear if the resampling step is skipped, which they proposed to do in rigid registration by computing the objective function using stochastic integration (instead of  ... 
doi:10.1109/tip.2012.2224356 pmid:23076044 pmcid:PMC3694571 fatcat:vzu6liuozjclno7ao4f3wsk2n4
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