Publications

2018
Stefanik L, Erdman L, Ameis SH, Foussias G, Mulsant BH, Behdinan T, Goldenberg A, O'Donnell LJ, Voineskos AN. Brain-Behavior Participant Similarity Networks Among Youth and Emerging Adults with Schizophrenia Spectrum, Autism Spectrum, or Bipolar Disorder and Matched Controls. Neuropsychopharmacology 2018;43(5):1180.
Sydnor VJ, Rivas-Grajales AM{\'ıa, Lyall AE, Zhang F, Bouix S, Karmacharya S, Shenton ME, Westin C-F, Makris N, Wassermann D, O'Donnell LJ, Kubicki M. A comparison of three fiber tract delineation methods and their impact on white matter analysis. NeuroImage 2018;
Gong S, Zhang F, Norton I, Essayed WI, Unadkat P, Rigolo L, Pasternak O, Rathi Y, Hou L, Golby AJ, O'Donnell LJ. Free water modeling of peritumoral edema using multi-fiber tractography: Application to tracking the arcuate fasciculus for neurosurgical planning. PloS one 2018;13(5):e0197056.
Hong Y, O'Donnell LJ, Savadjiev P, Zhang F, Wassermann D, Pasternak O, Johnson H, Paulsen J, Vonsattel J-P, Makris N, Westin C-F, Rathi Y. Genetic load determines atrophy in hand cortico-striatal pathways in presymptomatic Huntington's disease. Human Brain Mapping 2018;
Albi A, Meola A, Zhang F, Kahali P, Rigolo L, Tax CMW, Ciris PA, Essayed WI, Unadkat P, Norton I, Rathi Y, Olubiyi O, Golby AJ, O'Donnell LJ. Image Registration to Compensate for EPI Distortion in Patients with Brain Tumors: An Evaluation of Tract-Specific Effects. Journal of Neuroimaging 2018;
Zhang F, Wu W, Ning L, McAnulty G, Waber D, Gagoski B, Sarill K, Hamoda HM, Song Y, Cai W, Rathi Y, O'Donnell LJ. Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis. NeuroImage 2018;
Lyall AE, Savadjiev P, del Re EC, Seitz J, O’Donnell LJ, Westin C-F, Mesholam-Gately RI, Petryshen T, Wojcik JD, Nestor P, others. Utilizing Mutual Information Analysis to Explore the Relationship Between Gray and White Matter Structural Pathologies in Schizophrenia. Schizophrenia bulletin 2018;
2017
O'Donnell LJ, Daducci A, Wassermann D, Lenglet C. Advances in computational and statistical diffusion MRI. NMR in Biomedicine 2017;
Otake Y, Miyamoto K, Ollivier A, Yokota F, Fukuda N, O’Donnell LJ, Westin C-F, Takao M, Sugano N, Chung BS, others. Reconstruction of 3D Muscle Fiber Structure Using High Resolution Cryosectioned Volume. In: International Workshop and Challenge on Computational Methods and Clinical Applications in Musculoskeletal Imaging. Springer, Cham; 2017 p. 85–94.
Zhang F, Savadjiev P, Cai W, Song Y, Rathi Y, Tunç B, Parker D, Kapur T, Schultz RT, Makris N, Verma R, O'Donnell LJ. Whole brain white matter connectivity analysis using machine learning: an application to autism. NeuroImage 2017;
Song Y, Zhang F, Li Q, Huang H, O'Donnell LJ, Cai W. Locally-Transferred Fisher Vectors for Texture Classification. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 2017 p. 4912–4920.
Otake Y, Yokota F, Fukuda N, Takao M, Takagi S, Yamamura N, O’Donnell LJ, Westin C-F, Sugano N, Sato Y. Patient-Specific Skeletal Muscle Fiber Modeling from Structure Tensor Field of Clinical CT Images. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Cham; 2017 p. 656–663.
Zhang F, Wu W, Ning L, McAnulty G, Waber D, Gagoski B, Sarill K, Hamoda H, Song Y, Cai W, Rathi Y, O'Donnell LJ. Supra-threshold Fiber Cluster Statistics for Data-driven Whole Brain Tractography Analysis. In: International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI). 2017 p. 556-565.Abstract
Abstract. This work presents a supra-threshold fiber cluster (STFC) analysis that leverages the whole brain fiber geometry to enhance statistical group difference analysis. The proposed method consists of (1) a study-specific data-driven tractography parcellation to obtain white matter (WM) tract parcels according to the WM anatomy and (2) a nonparametric permutation-based STFC test to identify significant differences between study populations (e.g. disease and healthy). The basic idea of our method is that a WM parcel’s neighborhood (parcels with similar WM anatomy) can support the parcel’s statistical significance when correcting for multiple comparisons. The method is demonstrated by application to a multi-shell diffusion MRI dataset from 59 individuals, including 30 attention deficit hyperactivity disorder (ADHD) patients and 29 healthy controls (HCs). Evaluations are conducted using both synthetic and real data. The results indicate that our STFC method gives greater sensitivity in finding group differences in WM tract parcels compared to several traditional multiple comparison correction methods.
Zhang F, Kahali P, Suter Y, Norton I, Rigolo L, Savadjiev P, Song Y, Rathi Y, Cai W, Wells WM, Golby AJ, O’Donnell LJ. Automated connectivity-based groupwise cortical atlas generation: Application to data of neurosurgical patients with brain tumors for cortical parcellation prediction. In: Biomedical Imaging (ISBI 2017), 2017 IEEE 14th International Symposium on. IEEE; 2017 p. 774–777.
Liao R, Ning L, Chen Z, Rigolo L, Gong S, Pasternak O, Golby AJ, Rathi Y, O’Donnell LJ. Performance of unscented Kalman filter tractography in edema: Analysis of the two-tensor model. NeuroImage: Clinical 2017;15:819–831.
Norton I, Essayed WI, Zhang F, Pujol S, Yarmarkovich A, Golby AJ, Kindlmann G, Wasserman D, Johnson J, Westin C-F, O’Donnell LJ. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Research 2017;
Zhang F, Norton I, Cai W, Song Y, Wells WM, O'Donnell LJ. Comparison between two white matter segmentation strategies: An investigation into white matter segmentation consistency. In: Biomedical Imaging (ISBI 2017), 2017 IEEE 14th International Symposium on. IEEE; 2017 p. 796–799.
Shaffer JJ, Ghayoor A, Long JD, Kim RE-Y, Lourens S, O'Donnell LJ, Westin C-F, Rathi Y, Magnotta V, Paulsen JS, others. Longitudinal diffusion changes in prodromal and early HD: Evidence of white-matter tract deterioration. Human brain mapping 2017;38(3):1460–1477.
Essayed WI, Zhang F, Unadkat P, Cosgrove RG, Golby AJ, O'Donnell LJ. White matter tractography for neurosurgical planning: A topography-based review of the current state of the art. NeuroImage: Clinical 2017;
O’Donnell LJ, Suter Y, Rigolo L, Kahali P, Zhang F, Norton I, Albi A, Olubiyi O, Meola A, Essayed WI, Unadkat P, Ciris PA, Wells WM, Rathi Y, Westin C-F, Golby AJ. Automated white matter fiber tract identification in patients with brain tumors. NeuroImage: Clinical 2017;13:138–153.

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