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Fishbaugh, James; Gerig, Guido
The analysis of medical image time-series is becoming increasingly important as longitudinal imaging studies are maturing and large scale open imaging databases are becoming available. Image regression is widely used for several purposes: as a statistical representation for hypothesis testing, to bring clinical scores and images not acquired at the same time into temporal correspondence, or as a consistency filter to enforce temporal correlation. Geodesic image regression is the most prominent method, but the geodesic constraint limits the flexibility and therefore the application of the model, particularly when the observation time window is large or the anatomical changes are non-monotonic. In this paper, we propose to parameterize diffeomorphic flow by acceleration rather than velocity, as in the geodesic model. This results in a nonparametric image regression model which is completely flexible to capture complex change trajectories, while still constrained to be diffeomorphic and with a guarantee of temporal smoothness. We demonstrate the application of our model on synthetic 2D images as well as real 3D images of the cardiac cycle.
PMID: 31938451
ISSN: 1945-7928
CID: 4294612

Model selection for spatiotemporal modeling of early childhood sub-cortical development

Fishbaugh, James; Paniagua, Beatriz; Mostapha, Mahmoud; Styner, Martin; Murphy, Veronica; Gilmore, John; Gerig, Guido
Spatiotemporal shape models capture the dynamics of shape change over time and are an essential tool for monitoring and measuring anatomical growth or degeneration. In this paper we evaluate non-parametric shape regression on the challenging problem of modeling early childhood sub-cortical development starting from birth. Due to the flexibility of the model, it can be challenging to choose parameters which lead to a good model fit yet does not over fit. We systematically test a variety of parameter settings to evaluate model fit as well as the sensitivity of the method to specific parameters, and we explore the impact of missing data on model estimation.
PMID: 31073259
ISSN: 0277-786x
CID: 3903192

Multi-modal Image Fusion for Multispectral Super-resolution in Microscopy

Dey, Neel; Li, Shijie; Bermond, Katharina; Heintzmann, Rainer; Curcio, Christine A; Ach, Thomas; Gerig, Guido
Spectral imaging is a ubiquitous tool in modern biochemistry. Despite acquiring dozens to thousands of spectral channels, existing technology cannot capture spectral images at the same spatial resolution as structural microscopy. Due to partial voluming and low light exposure, spectral images are often difficult to interpret and analyze. This highlights a need to upsample the low-resolution spectral image by using spatial information contained in the high-resolution image, thereby creating a fused representation with high specificity both spatially and spectrally. In this paper, we propose a framework for the fusion of co-registered structural and spectral microscopy images to create super-resolved representations of spectral images. As a first application, we super-resolve spectral images of retinal tissue imaged with confocal laser scanning microscopy, by using spatial information from structured illumination microscopy. Second, we super-resolve mass spectroscopic images of mouse brain tissue, by using spatial information from high-resolution histology images. We present a systematic validation of model assumptions crucial towards maintaining the original nature of spectra and the applicability of super-resolution. Goodness-of-fit for spectral predictions are evaluated through functional R2 values, and the spatial quality of the super-resolved images are evaluated using normalized mutual information.
PMID: 31777411
ISSN: 0277-786x
CID: 4216552

Analysis of the kinematic motion of the wrist from 4D magnetic resonance imaging

Chapter by: Abbas, Batool; Fishbaugh, James; Petchprapa, Catherine; Lattanzi, Riccardo; Gerig, Guido
in: Progress in Biomedical Optics and Imaging - Proceedings of SPIE by
[S.l.] :, 2019
pp. ?-?
ISBN: 9781510625457
CID: 4008682

User-Guided Segmentation of Multi-modality Medical Imaging Datasets with ITK-SNAP

Yushkevich, Paul A; Pashchinskiy, Artem; Oguz, Ipek; Mohan, Suyash; Schmitt, J Eric; Stein, Joel M; Zukić, Dženan; Vicory, Jared; McCormick, Matthew; Yushkevich, Natalie; Schwartz, Nadav; Gao, Yang; Gerig, Guido
ITK-SNAP is an interactive software tool for manual and semi-automatic segmentation of 3D medical images. This paper summarizes major new features added to ITK-SNAP over the last decade. The main focus of the paper is on new features that support semi-automatic segmentation of multi-modality imaging datasets, such as MRI scans acquired using different contrast mechanisms (e.g., T1, T2, FLAIR). The new functionality uses decision forest classifiers trained interactively by the user to transform multiple input image volumes into a foreground/background probability map; this map is then input as the data term to the active contour evolution algorithm, which yields regularized surface representations of the segmented objects of interest. The new functionality is evaluated in the context of high-grade and low-grade glioma segmentation by three expert neuroradiogists and a non-expert on a reference dataset from the MICCAI 2013 Multi-Modal Brain Tumor Segmentation Challenge (BRATS). The accuracy of semi-automatic segmentation is competitive with the top specialized brain tumor segmentation methods evaluated in the BRATS challenge, with most results obtained in ITK-SNAP being more accurate, relative to the BRATS reference manual segmentation, than the second-best performer in the BRATS challenge; and all results being more accurate than the fourth-best performer. Segmentation time is reduced over manual segmentation by 2.5 and 5 times, depending on the rater. Additional experiments in interactive placenta segmentation in 3D fetal ultrasound illustrate the generalizability of the new functionality to a different problem domain.
PMID: 29946897
ISSN: 1559-0089
CID: 3163142

Restricted and Repetitive Behavior and Brain Functional Connectivity in Infants at Risk for Developing Autism Spectrum Disorder

McKinnon, Claire J; Eggebrecht, Adam T; Todorov, Alexandre; Wolff, Jason J; Elison, Jed T; Adams, Chloe M; Snyder, Abraham Z; Estes, Annette M; Zwaigenbaum, Lonnie; Botteron, Kelly N; McKinstry, Robert C; Marrus, Natasha; Evans, Alan; Hazlett, Heather C; Dager, Stephen R; Paterson, Sarah J; Pandey, Juhi; Schultz, Robert T; Styner, Martin A; Gerig, Guido; Schlaggar, Bradley L; Petersen, Steven E; Piven, Joseph; Pruett, John R
BACKGROUND:Restricted and repetitive behaviors (RRBs), detectable by 12 months in many infants in whom autism spectrum disorder (ASD) is later diagnosed, may represent some of the earliest behavioral markers of ASD. However, brain function underlying the emergence of these key behaviors remains unknown. METHODS:Behavioral and resting-state functional connectivity (fc) magnetic resonance imaging data were collected from 167 children at high and low familial risk for ASD at 12 and 24 months (n = 38 at both time points). Twenty infants met criteria for ASD at 24 months. We divided RRBs into four subcategories (restricted, stereotyped, ritualistic/sameness, self-injurious) and used a data-driven approach to identify functional brain networks associated with the development of each RRB subcategory. RESULTS:Higher scores for ritualistic/sameness behavior were associated with less positive fc between visual and control networks at 12 and 24 months. Ritualistic/sameness and stereotyped behaviors were associated with less positive fc between visual and default mode networks at 12 months. At 24 months, stereotyped and restricted behaviors were associated with more positive fc between default mode and control networks. Additionally, at 24 months, stereotyped behavior was associated with more positive fc between dorsal attention and subcortical networks, whereas restricted behavior was associated with more positive fc between default mode and dorsal attention networks. No significant network-level associations were observed for self-injurious behavior. CONCLUSIONS:These observations mark the earliest known description of functional brain systems underlying RRBs, reinforce the construct validity of RRB subcategories in infants, and implicate specific neural substrates for future interventions targeting RRBs.
PMID: 30446435
ISSN: 2451-9030
CID: 3500772

Longitudinal structural connectivity in the developing brain with projective non-negative matrix factorization

Heejong Kim; Piven, J.; Gerig, G.
Understanding of early brain changes has the potential to investigate imaging biomarkers for pre-symptomatic diagnosis and thus opportunity for optimal therapeutic intervention, for example in early diagnosis of infants at risk to autism or altered development of infants to drug exposure. In this paper, we propose a framework to analyze longitudinal changes of structural connectivity in the early developing infant brain by exploring underlying network components of brain structural connectivity and its changes with age. Structural connectivity is a non-negative sparse network. Projective non-negative matrix factorization (PNMF) offers benefits in sparsity and learning fewer parameters for non-negative sparse data. The number of matrix subcomponents was estimated by automatic relevance determination PNMF (ARDPNMF) for brain connectivity networks for the given data. We apply linear mixed effect modeling on the resulting loadings from ARDPNMF to model longitudinal network component changes over time. The proposed framework was validated on a synthetic example generated by known linear mixed effects on loadings of the known number of bases with different levels of additive noises. Feasibility of the framework on real data has been demonstrated by analysis of structural connectivity networks of high angular resonance diffusion imaging (HARDI) data from an ongoing neuroimaging study of autism. A total of 139 image data sets from high-risk and low-risk subjects acquired at multiple time points have been processed. Results demonstrate the feasibility of the framework to analyze connectivity network properties as a function of age and the potential to eventually explore differences associated with risk status
ISSN: 1605-7422
CID: 4085852

Analysis of Morphological Changes of Lamina Cribrosa Under Acute Intraocular Pressure Change

Ravier, Mathilde; Hong, Sungmin; Girot, Charly; Ishikawa, Hiroshi; Tauber, Jenna; Wollstein, Gadi; Schuman, Joel; Fishbaugh, James; Gerig, Guido
Glaucoma is the second leading cause of blindness world-wide. Despite active research efforts driven by the importance of diagnosis and treatment of the optic degenerative neuropathy, the relationship between structural and functional changes along the glaucomateous evolution are still not clearly understood. Dynamic changes of the lamina cribrosa (LC) in the presence of intraocular pressure (IOP) were suggested to play a significant role in optic nerve damage, which motivates the proposed research to explore the relationship of changes of the 3D structure of the LC collagen meshwork to clinical diagnosis. We introduce a framework to quantify 3D dynamic morphological changes of the LC under acute IOP changes in a series of swept-source optical coherence tomography (SS-OCT) scans taken under different pressure states. Analysis of SS-OCT images faces challenges due to low signal-to-noise ratio, anisotropic resolution, and observation variability caused by subject and ocular motions. We adapt unbiased diffeomorphic atlas building which serves multiple purposes critical for this analysis. Analysis of deformation fields yields desired global and local information on pressure-induced geometric changes. Deformation variability, estimated with repeated images of a healthy volunteer without IOP elevation, is found to be a magnitude smaller than pressure-induced changes and thus illustrates feasibility of the proposed framework. Results in a clinical study with healthy, glaucoma suspect, and glaucoma subjects demonstrate the potential of the proposed method for non-invasive in vivo analysis of LC dynamics, potentially leading to early prediction and diagnosis of glaucoma.
PMID: 32656546
ISSN: n/a
CID: 4552712

Stability Analysis of Lamina Cribrosa Structure in Repeated Optical Coherence Tomography Scans [Meeting Abstract]

Fishbaugh, James; Hong, Sungmin; Ishikawa, Hiroshi; Ravier, Mathilde; Wollstein, Gadi; Schuman, Joel S.; Gerig, Guido
ISSN: 0146-0404
CID: 3333502

Groupwise 3D Nonlinear Registration of OCT Image Series for Analyzing Dynamic Lamina Cribrosa Changes [Meeting Abstract]

Hong, Sungmin; Ravier, Mathilde; Ishikawa, Hiroshi; Girot, Charly; Tauber, Jenna; Wollstein, Gadi; Schuman, Joel S.; Fishbaugh, James; Gerig, Guido
ISSN: 0146-0404
CID: 3333512