Jeremy Magland

Publications

  • Ward B, Soules J, Magland J. Stan Playground: Run Stan models directly in your browser. Journal of Open Source Software, 2026. doi:10.21105/joss.09531

  • Lee KH, Denovellis EL, Ly R, Magland J, Soules J, Comrie AE, Gramling DP, Guidera JA, Nevers R, Adenekan P, et al. Spyglass: a framework for reproducible and shareable neuroscience research. eLife, 2026. doi:10.7554/eLife.108089

  • Magland JF, Ly R, Rübel O, Dichter B. Facilitating analysis of open neurophysiology data on the DANDI Archive using large language model tools. Nature Scientific Data, 2025. doi:10.1038/s41597-025-06285-x

  • Magland J, Soules J, Baker C, Dichter B. Neurosift: DANDI exploration and NWB visualization in the browser. Journal of Open Source Software, 2024. doi:10.21105/joss.06590

  • Buccino AP, Hurwitz CL, Garcia S, Magland J, Siegle JH, Hurwitz R, Hennig MH. SpikeInterface, a unified framework for spike sorting. eLife, 2020. doi:10.7554/eLife.61834

  • Magland J, Jun JJ, Lovero E, Morley AJ, Hurwitz CL, Buccino AP, Garcia S, Barnett AH. SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters. eLife, 2020. doi:10.7554/eLife.55167

  • Barnett A, Epstein CL, Greengard L, Magland J. Geometry of the phase retrieval problem. Inverse Problems, 2020. doi:10.1088/1361-6420/aba5ed

  • Barmherzig D, Barnett AB, Epstein CL, Greengard LF, Magland JF, Rachh M. Recovering missing data in coherent diffraction imaging. 2020. arXiv:2002.02874

  • Leonard MB, Wehrli FW, Ziolkowski SL, Billig E, Long J, Nickolas TL, Magland JF, Nihtianova S, Zemel BS, Herskovitz R, et al. A multi-imaging modality study of bone density, bone structure and the muscle - bone unit in end-stage renal disease. Bone, 2019. doi:10.1016/j.bone.2019.05.022

  • Chung JE, Joo HR, Fan JL, …, Magland JF, et al. High-Density, Long-Lasting, and Multi-region Electrophysiological Recordings Using Polymer Electrode Arrays. Neuron, 2019. doi:10.1016/j.neuron.2018.11.002

  • Barnett AH, Magland JF, af Klinteberg L. A parallel non-uniform fast Fourier transform library based on an “exponential of semicircle” kernel. 2018. arXiv:1808.06736

  • Chung JE, Magland JF, Barnett AH, Tolosa VM, Tooker AC, Lee KY, Shah KG, Felix SH, Frank LM, Greengard LF. A Fully Automated Approach to Spike Sorting. Neuron, 2017. doi:10.1016/j.neuron.2017.08.030

  • Li C, Magland JF, Zhao X, Seifert AC, Wehrli FW. Selective in vivo bone imaging with long-T2 suppressed PETRA MRI. Magnetic Resonance in Medicine, 2017. doi:10.1002/mrm.26178

  • Barnett AH, Magland JF, Greengard LF. Validation of neural spike sorting algorithms without ground-truth information. Journal of neuroscience methods, 2016. doi:10.1016/j.jneumeth.2016.02.022

  • Magland JF, Li C, Langham MC, Wehrli FW. Pulse sequence programming in a dynamic visual environment: SequenceTree. Magnetic Resonance in Medicine, 2016. doi:10.1002/mrm.25640

  • Barhoum S, Langham MC, Magland JF, Rodgers ZB, Li C, Rajapakse CS, Wehrli FW. Method for rapid MRI quantification of global cerebral metabolic rate of oxygen. Journal of Cerebral Blood Flow and Metabolism, 2015. doi:10.1038/jcbfm.2015.96

  • Langham MC, Zhou Y, Chirico EN, Magland JF, Sehgal CM, Englund EK, Mohler ER, Guo W, Barhoum S, Wehrli FW. Effects of age and smoking on endothelial function assessed by quantitative cardiovascular magnetic resonance in the peripheral and central vasculature. Journal of Cardiovascular Magnetic Resonance, 2015. doi:10.1186/s12968-015-0110-8

  • Mostoufi-Moab S, Magland J, Isaacoff EJ, Sun W, Rajapakse CS, Zemel B, Wehrli F, Shekdar K, Baker J, Long J, et al. Adverse Fat Depots and Marrow Adiposity Are Associated With Skeletal Deficits and Insulin Resistance in Long-Term Survivors of Pediatric Hematopoietic Stem Cell Transplantation. Journal of Bone and Mineral Research, 2015. doi:10.1002/jbmr.2512

  • Rodgers ZB, Englund EK, Langham MC, Magland JF, Wehrli FW. Rapid T2- and susceptometry-based CMRO2 quantification with interleaved TRUST (iTRUST). NeuroImage, 2015. doi:10.1016/j.neuroimage.2014.10.061

  • Barhoum S, Rodgers ZB, Langham M, Magland JF, Li C, Wehrli FW. Comparison of MRI methods for measuring whole-brain venous oxygen saturation. Magnetic Resonance in Medicine, 2015. doi:10.1002/mrm.25336

  • Zhang N, Magland JF, Song HK, Wehrli FW. Registration-based autofocusing technique for automatic correction of motion artifacts in time-series studies of high-resolution bone MRI. Journal of Magnetic Resonance Imaging, 2015. doi:10.1002/jmri.24646

  • Magland JF, Barnett AH. Unimodal clustering using isotonic regression: ISO-SPLIT. 2015. arXiv:1508.04841

  • Li C, Magland JF, Seifert AC, Wehrli FW. Correction of excitation profile in Zero Echo Time (ZTE) imaging using quadratic phase-modulated RF pulse excitation and iterative reconstruction. IEEE Transactions on Medical Imaging, 2014. doi:10.1109/TMI.2014.2300500

  • Wehrli FW, Rodgers ZB, Jain V, Langham MC, Li C, Licht DJ, Magland J. Time-resolved MRI oximetry for quantifying CMRO(2) and vascular reactivity. Academic Radiology, 2014. doi:10.1016/j.acra.2013.11.001

  • Rajapakse CS, Phillips EA, Sun W, Wald MJ, Magland JF, Snyder PJ, Wehrli FW. Vertebral deformities and fractures are associated with MRI and pQCT measures obtained at the distal tibia and radius of postmenopausal women. Osteoporosis International, 2014. doi:10.1007/s00198-013-2569-1

  • Cortes DH, Magland JF, Wright AC, Elliott DM. The shear modulus of the nucleus pulposus measured using magnetic resonance elastography: a potential biomarker for intervertebral disc degeneration. Magnetic Resonance in Medicine, 2014. doi:10.1002/mrm.24895

  • Magland JF, Childress AR. Task-correlated facial and head movements in classifier-based real-time FMRI. Journal of Neuroimaging, 2014. doi:10.1111/jon.12015

  • Zhang N, Magland JF, Rajapakse CS, Lam SB, Wehrli FW. Assessment of trabecular bone yield and post-yield behavior from high-resolution MRI-based nonlinear finite element analysis at the distal radius of premenopausal and postmenopausal women susceptible to osteoporosis. Academic Radiology, 2013. doi:10.1016/j.acra.2013.09.005

  • Zhang N, Magland JF, Rajapakse CS, Bhagat YA, Wehrli FW. Potential of in vivo MRI-based nonlinear finite-element analysis for the assessment of trabecular bone post-yield properties. Medical Physics, 2013. doi:10.1118/1.4802085

  • Jain V, Magland J, Langham M, Wehrli FW. High temporal resolution in vivo blood oximetry via projection-based T2 measurement. Magnetic Resonance in Medicine, 2013. doi:10.1002/mrm.24519

  • Lam SC, Wang Z, Li Y, Franklin T, O’Brien C, Magland J, Childress AR. Wavelet-transformed temporal cerebral blood flow signals during attempted inhibition of cue-induced cocaine craving distinguish prognostic phenotypes. Drug and Alcohol Dependence, 2013. doi:10.1016/j.drugalcdep.2012.08.018

  • Magland JF, Zhang N, Rajapakse CS, Wehrli FW. Computationally-optimized bone mechanical modeling from high-resolution structural images. PLOS ONE, 2012. doi:10.1371/journal.pone.0035525

  • Rajapakse CS, Leonard MB, Bhagat YA, Sun W, Magland JF, Wehrli FW. Micro-MR imaging-based computational biomechanics demonstrates reduction in cortical and trabecular bone strength after renal transplantation. Radiology, 2012. doi:10.1148/radiol.11111044

  • Wald MJ, Magland JF, Rajapakse CS, Bhagat YA, Wehrli FW. Predicting trabecular bone elastic properties from measures of bone volume fraction and fabric on the basis of micromagnetic resonance images. Magnetic Resonance in Medicine, 2012. doi:10.1002/mrm.23253

  • Li C, Magland JF, Rad HS, Song HK, Wehrli FW. Comparison of optimized soft-tissue suppression schemes for ultrashort echo time MRI. Magnetic Resonance in Medicine, 2012. doi:10.1002/mrm.23267

  • Li C, Langham MC, Epstein CL, Magland JF, Wu J, Gee J, Wehrli FW. Accuracy of the cylinder approximation for susceptometric measurement of intravascular oxygen saturation. Magnetic Resonance in Medicine, 2012. doi:10.1002/mrm.23034

  • Bhagat YA, Rajapakse CS, Magland JF, Wald MJ, Song HK, Leonard MB, Wehrli FW. On the significance of motion degradation in high-resolution 3D μMRI of trabecular bone. Academic Radiology, 2011. doi:10.1016/j.acra.2011.06.006

  • Jain V, Langham MC, Floyd TF, Jain G, Magland JF, Wehrli FW. Rapid magnetic resonance measurement of global cerebral metabolic rate of oxygen consumption in humans during rest and hypercapnia. Journal of Cerebral Blood Flow and Metabolism, 2011. doi:10.1038/jcbfm.2011.34

  • Wright AC, Lemdiasov R, Connick TJ, Bhagat YA, Magland JF, Song HK, Toddes SP, Ludwig R, Wehrli FW. Helmholtz-pair transmit coil with integrated receive array for high-resolution MRI of trabecular bone in the distal tibia at 7T. Journal of Magnetic Resonance, 2011. doi:10.1016/j.jmr.2011.02.019

  • Bhagat YA, Rajapakse CS, Magland JF, Love JH, Wright AC, Wald MJ, Song HK, Wehrli FW. Performance of μMRI-Based virtual bone biopsy for structural and mechanical analysis at the distal tibia at 7T field strength. Journal of Magnetic Resonance Imaging, 2011. doi:10.1002/jmri.22439

  • Rad HS, Lam SC, Magland JF, Ong H, Li C, Song HK, Love J, Wehrli FW. Quantifying cortical bone water in vivo by three-dimensional ultra-short echo-time MRI. NMR in Biomedicine, 2011. doi:10.1002/nbm.1631

  • Magland JF, Tjoa CW, Childress AR. Spatio-temporal activity in real time (STAR): optimization of regional fMRI feedback. NeuroImage, 2011. doi:10.1016/j.neuroimage.2010.12.085

  • Langham MC, Li C, Magland JF, Wehrli FW. Nontriggered MRI quantification of aortic pulse-wave velocity. Magnetic Resonance in Medicine, 2011. doi:10.1002/mrm.22651

  • Rajapakse CS, Magland JF, Wald MJ, Liu XS, Zhang XH, Guo XE, Wehrli FW. Computational biomechanics of the distal tibia from high-resolution MR and micro-CT images. Bone, 2010. doi:10.1016/j.bone.2010.05.039

  • Langham MC, Jain V, Magland JF, Wehrli FW. Time-resolved absolute velocity quantification with projections. Magnetic Resonance in Medicine, 2010. doi:10.1002/mrm.22559

  • Vandoorne K, Magland J, Plaks V, Sharir A, Zelzer E, Wehrli F, Hemmings BA, Harmelin A, Neeman M. Bone vascularization and trabecular bone formation are mediated by PKB alpha/Akt1 in a gene-dosage-dependent manner: in vivo and ex vivo MRI. Magnetic Resonance in Medicine, 2010. doi:10.1002/mrm.22395

  • Liu XS, Zhang XH, Rajapakse CS, Wald MJ, Magland J, Sekhon KK, Adam MF, Sajda P, Wehrli FW, Guo XE. Accuracy of high-resolution in vivo micro magnetic resonance imaging for measurements of microstructural and mechanical properties of human distal tibial bone. Journal of Bone and Mineral Research, 2010. doi:10.1002/jbmr.92

  • Wald MJ, Magland JF, Rajapakse CS, Wehrli FW. Structural and mechanical parameters of trabecular bone estimated from in vivo high-resolution magnetic resonance images at 3 tesla field strength. Journal of Magnetic Resonance Imaging, 2010. doi:10.1002/jmri.22158

  • Wehrli FW, Rajapakse CS, Magland JF, Snyder PJ. Mechanical implications of estrogen supplementation in early postmenopausal women. Journal of Bone and Mineral Research, 2010. doi:10.1002/jbmr.33

  • Magland JF, Rajapakse CS, Wright AC, Acciavatti R, Wehrli FW. 3D fast spin echo with out-of-slab cancellation: a technique for high-resolution structural imaging of trabecular bone at 7 Tesla. Magnetic Resonance in Medicine, 2010. doi:10.1002/mrm.22213

  • Langham MC, Floyd TF, Mohler ER, Magland JF, Wehrli FW. Evaluation of cuff-induced ischemia in the lower extremity by magnetic resonance oximetry. Journal of the American College of Cardiology, 2010. doi:10.1016/j.jacc.2009.08.068

  • Anumula S, Wehrli SL, Magland J, Wright AC, Wehrli FW. Ultra-short echo-time MRI detects changes in bone mineralization and water content in OVX rat bone in response to alendronate treatment. Bone, 2010. doi:10.1016/j.bone.2010.01.372

  • Witschey WR, Borthakur A, Elliott MA, Magland J, McArdle EL, Wheaton A, Reddy R. Spin-locked balanced steady-state free-precession (slSSFP). Magnetic Resonance in Medicine, 2009. doi:10.1002/mrm.22092

  • Langham MC, Magland JF, Epstein CL, Floyd TF, Wehrli FW. Accuracy and precision of MR blood oximetry based on the long paramagnetic cylinder approximation of large vessels. Magnetic Resonance in Medicine, 2009. doi:10.1002/mrm.21981

  • Rajapakse CS, Magland J, Zhang XH, Liu XS, Wehrli SL, Guo XE, Wehrli FW. Implications of noise and resolution on mechanical properties of trabecular bone estimated by image-based finite-element analysis. Journal of Orthopaedic Research, 2009. doi:10.1002/jor.20877

  • Magland JF, Wald MJ, Wehrli FW. Spin-echo micro-MRI of trabecular bone using improved 3D fast large-angle spin-echo (FLASE). Magnetic Resonance in Medicine, 2009. doi:10.1002/mrm.21905

  • Langham MC, Magland JF, Floyd TF, Wehrli FW. Retrospective correction for induced magnetic field inhomogeneity in measurements of large-vessel hemoglobin oxygen saturation by MR susceptometry. Magnetic Resonance in Medicine, 2009. doi:10.1002/mrm.21499

  • Magland JF, Jones CE, Leonard MB, Wehrli FW. Retrospective 3D registration of trabecular bone MR images for longitudinal studies. Journal of Magnetic Resonance Imaging, 2009. doi:10.1002/jmri.21551

  • Magland JF. Discrete inverse scattering theory for NMR pulse design. 2009. arXiv:0903.4363

  • Li CQ, Magland JF, Rajapakse CS, Guo XE, Zhang XH, Vasilic B, Wehrli FW. Implications of resolution and noise for in vivo micro-MRI of trabecular bone. Medical Physics, 2008. doi:10.1118/1.3005598

  • Magland JF, Wehrli FW. Trabecular bone structure analysis in the limited spatial resolution regime of in vivo MRI. Academic Radiology, 2008. doi:10.1016/j.acra.2008.05.015

  • Rajapakse CS, Magland JF, Wehrli FW. Fast prospective registration of in vivo MR images of trabecular bone microstructure in longitudinal studies. Magnetic Resonance in Medicine, 2008. doi:10.1002/mrm.21593

  • Wehrli FW, Ladinsky GA, Jones C, Benito M, Magland J, Vasilic B, Popescu AM, Zemel B, Cucchiara AJ, Wright AC, et al. In vivo magnetic resonance detects rapid remodeling changes in the topology of the trabecular bone network after menopause and the protective effect of estradiol. Journal of Bone and Mineral Research, 2008. doi:10.1359/jbmr.080108

  • Anumula S, Magland J, Wehrli SL, Ong H, Song HK, Wehrli FW. Multi-modality study of the compositional and mechanical implications of hypomineralization in a rabbit model of osteomalacia. Bone, 2008. doi:10.1016/j.bone.2007.10.011

  • Anumula S, Magland J, Wehrli SL, Zhang H, Ong H, Song HK, Wehrli FW. Measurement of phosphorus content in normal and osteomalacic rabbit bone by solid-state 3D radial imaging. Magnetic Resonance in Medicine, 2006. doi:10.1002/mrm.21050

  • Epstein CL, Magland J. A novel technique for imaging with inhomogeneous fields. Journal of Magnetic Resonance, 2006. doi:10.1016/j.jmr.2006.08.012

  • Magland J, Wehrli FW. General algorithm for automated off-center MRI. Magnetic Resonance in Medicine, 2006. doi:10.1002/mrm.20933

  • Magland J, Vasilic B, Wehrli FW. Fast low-angle dual spin-echo (FLADE): a new robust pulse sequence for structural imaging of trabecular bone. Magnetic Resonance in Medicine, 2006. doi:10.1002/mrm.20789

  • Techawiboonwong A, Song HK, Magland JF, Saha PK, Wehrli FW. Implications of pulse sequence in structural imaging of trabecular bone. Journal of Magnetic Resonance Imaging, 2005. doi:10.1002/jmri.20432

  • Magland J, Epstein CL. Practical pulse synthesis via the discrete inverse scattering transform. Journal of Magnetic Resonance, 2005. doi:10.1016/j.jmr.2004.09.022

  • Magland J, Epstein CL. Exact half pulse synthesis via the inverse scattering transform. Journal of Magnetic Resonance, 2004. doi:10.1016/j.jmr.2004.09.004