bib PDF open source code / software video abstract
† co-first authors; ‡ co-senior authors.
Letters to the Editors
2023
- T. Aung, N. Ikegaya, L. Mayoglou, J. Li, J. Martinez-Gonzalez,
“Prospective analysis of the multimodal invasive and noninvasive post-processing analyses in the surgical treatment of MRI-negative occiptal lobe epilepsy”,
Clinical Neurophysiology, vol. 155, pp. 55–57, 2023.
Conference Abstracts
2027
- H. J. Freeman, J. A. Yeager, M. J. Young, B. L. Edlow, J. Li‡, M. Fecchio‡,
“CT-to-MRI synthesis for neuronavigation in noninvasive brain stimulation”,
7th International Brain Stimulation Conference, Lyon, France, Feb. 2027. (Submitted)
2026
A. Sterling, J. Lew, M. Monti, C. Schnakers, M. Fecchio, B. Guerin, J. Li, D. Schreier, B. Edlow, M. Young,
“Toward an ethical framework for transcranial focused ultrasound neuromodulation in disorders of consciousness”,
103rd American Congress of Rehabilitation Medicine Annual Conference, Washington, DC, Oct. 2026.- A. Sterling, J. Lew, M. Monti, C. Schnakers, M. Fecchio, B. Guerin, J. Li, D. Schreier, B. Edlow, M. Young,
“Toward an ethical framework for transcranial focused ultrasound neuromodulation in disorders of consciousness”,
24th Neurocritical Care Annual Meeting, Seattle, WA, Oct. 2026.Abstract
Background and Purpose: Transcranial focused ultrasound stimulation (tFUS) carries promise as a novel therapeutic tool to promote recovery of consciousness following brain injury through noninvasive, targeted neuromodulation of deep thalamic connectivity hubs. However, the novelty of this approach and its attendant effects raise a host of underexplored ethical considerations that warrant explicit attention. To better understand the considerations unique to individuals with disorders of consciousness (DoC), we aim to develop an ethical framework for responsible translation of this emerging neurotechnology. Methods: To identify and critically evaluate the responsible use of tFUS to promote recovery of consciousness in individuals with DoC, we examine ethical considerations through the lens of the principles of biomedical ethics: respect for autonomy, beneficence, nonmaleficence, and justice, coupled with thematic, normative and philosophical analysis. Results: Respect for autonomy requires structured attention to questions regarding moral distress, reemergence of agency, potential for therapeutic misconception, and careful disclosure of investigational results. The principles of beneficence and nonmaleficence require evaluation of the perception of risk, as well as balancing and communicating potentially atypical and often unknown long-term effects. Justice considerations call for attention to equitable access, post-trial obligations, and sharing of brain data among DoC stakeholders. Conclusion:Specific domains synergistically inform an ethical framework for stakeholders involved in pioneering and early use of tFUS. While centered on tFUS for DoC, the considerations identified carry broader applications to other areas of translational neuromodulation research. To provide support for clinicians and investigators navigating complex decision-making at the nexus of neurotechnology and neuroethics, we propose a practical checklist for ethical implementation and evaluation of tFUS studies for patients with DoC. Future work is needed to investigate perspectives of patients and families on the development and deployment of frontier neuromodulation neurotechnologies.
S. Choi, V. Vasudev, L. Kelley-Quon, R. M. Leahy, A. A. Joshi, J. Li, V. Rajagopalan, J. L. Wisnowski,
“Emergence of anti-correlated functional networks in neonates: Initial results from HBCD release 1.0”,
HEALthy Brain and ChildDevelopment (HBCD) Annual Meeting, Virtual, Mar. 2026.P. Klimes, P. Bosque, I. Dolezalova, L. Wadi, M. Moye, K. Jaber, Y. Zhu, J. Stuart, T. Aung, J. Li, J. Gotman, D. Southwell, D. Carlson, B. Frauscher,
“Deep phenotyping with unsupervised clustering reveals new subtypes of temporal lobe epilepsy”,
4th Artificial Intelligence in Epilepsy and Neurological Disorders Conference, San Juan, Mar. 2026.S. Choi, V. Vasudev, L. Kelley-Quon, R. M. Leahy, A. A. Joshi, J. Li, V. Rajagopalan, J. L. Wisnowski,
“NeoSync: Preliminary atlases of synchronized neonatal fMRI data derived from HBCD release 1.0”,
32th Annual Meeting of the Organization for Human Brain Mapping, Bordeaux, France, Jun. 2026.S. Choi, V. Vasudev, L. Kelley-Quon, R. M. Leahy, A. A. Joshi, J. Li, V. Rajagopalan, J. L. Wisnowski,
“Early life developmental functional connectivity changes in anti-correlated networks using HBCD Release 1.0”,
32th Annual Meeting of the Organization for Human Brain Mapping, Bordeaux, France, Jun. 2026.- M. K. Cambareri, H. J. Freman, D. Schreier, J. A. Yeager, S. Bruno, J. Li‡, B. L. Edlow‡, M. Fecchio‡,
“Resting-state functional connectivity predicts TMS-EEG-derived brain complexity”,
32th Annual Meeting of the Organization for Human Brain Mapping, Bordeaux, France, Jun. 2026.
2025
B. Coughlin, A. Paulk, P. Hadar, J. Li, D. Rubin, L. Hochberg, Z. Williams, S. Cash,
“A pipeline for 3D-printing full-scale brains and skulls in high resolution using imaging data”,
2025 MGB Neurology Research Retreat, Boston, MA, Jul. 2025.C. Belly, T. Aung, J. Li, T. Tumnark, J. Gonzalez-Martinez, B. Frauscher,
“Neuronal coupling between subcortical structure and temporal lobe structures in patients with drug resistant temporal lobe epilepsy”,
79th Annual Meeting of the American Epilepsy Society, Atlanta, GA, Dec. 2025.D. S. Jin, B. B. Ayvaz, J. R. Wheelock, J. Appleton, J. Li, L. J. Hirsch, B. Omay, S. F. Zafar, A. F. Struck, A. V. Dalca, B. L. Edlow, M. B. Westover, E. J. Gilmore, J. A. Kim,
“Acute phase magnetic resonance imaging (MRI) measurements predict post traumatic epilepsy (PTE) and functional outcome after traumatic brain injury (TBI)”,
79th Annual Meeting of the American Epilepsy Society, Atlanta, GA, Dec. 2025.D. S. Jin, B. B. Ayvaz, J. R. Wheelock, J. Appleton, J. Li, L. J. Hirsch, B. Omay, S. F. Zafar, A. F. Struck, A. V. Dalca, B. L. Edlow, M. B. Westover, E. J. Gilmore, J. A. Kim,
“Cortical measurements from acute phase magnetic resonance imaging (MRI) predict post-traumatic epilepsy (PTE)”,
54th Annual Meeting of the Society for Neuroscience, San Diego, CA, Nov. 2025.B. L. Edlow, M. E. Barra, D. R. Schreier, M. Fecchio, H. J. Freeman, J. Li, P. K. Lawrence, W. R. Sanders, A. Meydan, M. Masood, J. E. Kirsch, T. P. Bleck, J. J. Fins, G. J. T., L. R. Hochberg, B. C. Healy, K. Solt, E. N. Brown, Y. G. Bodien,
“Intravenous methylphenidate for acute traumatic disorders of consciousness: a phase 1, open-label, safety and dose-finding study”,
42nd Annual Symposium of National Neurotrauma Society, Philadelphia, PA, Jun. 2025.Y. Mantilla-Ramos, K. Jerbi, J. Li, D. Nair, R. M. Leahy,
“Using complexity and machine-learning to determine the epileptogenic zone in drug-resistant epilepsy”,
46th International Conference for Technology and Analysis of Seizures, Montreal, Quebec, Canada, Jun. 2025.D. R. Schreier, M. Fecchio, M. E. Barra, H. J. Freeman, J. Li, B. Healy, P. K. Lawrence, W. R. Sanders, A. Meydan, M. Masood, J. E. Kirsch, T. P. Bleck, J. J. Fins, G. J. T., L. R. Hochberg, K. Solt, E. N. Brown, Y. G. Bodien, B. L. Edlow,
“Electroencephalographic and behavioral findings from a phase 1 trial using intravenousmethylphenidate to promote consciousness in patients with acute traumatic brain injury”,
Consciousness, Anesthesia and Evolutionary Biology Gordon Research Conference, Lucca, Tuscany, Italy, Jan. 2025.
2024
M. K. Cambareri, J. Li‡, B. E. Edlow‡,
“Subcortical regions associated with consciousness level have high measures of resting state functional network integration”,
Neurocritical Care Society 22nd Annual Meeting, San Diego, CA, Oct. 2024.H. J. Freeman, A. S. Atalay, J. Li, N. Gilmore, S. B. Snider, H. Carrington, E. Selmanovic, A. Pruyser, L. Bura, B. R. Diamond, A. C. Seifert, D. Hunt, Y. G. Bodien, J. Hoffman, C. L. MacDonald, K. Dams-O’Connor‡, B. L. Edlow‡,
“Longitudinal lesion expansion in chronic traumatic brain injury”,
41st Annual Symposium of National Neurotrauma Society, San Francisco, CA, Jun. 2024.M. Öncel, J. H. Lai, J. Li, S. A. Aykan, J. Yang, T. Qin, A. Harriott, D. Boas, S. Sakadžić, C. Ayata, B. L. Edlow, D. Y. Chung,
“Functional neuronal networks after cortical spreading depolarizations”,
76th Annual Meeting of American Academy of Neurology, Denver, CO, Apr. 2024.
2023
Y. Mantilla-Ramos, J. Li, D. Nair, P. Chauvel, K. Jerbi, R. M. Leahy,
“SEEG-based localization of the epileptogenic zone from complexity measures using machine learning”,
77th Annual Meeting of the American Epilepsy Society, Orlando, FL, Dec. 2023.M. Öncel, J. H. Lai, J. Li, S. A. Aykan, J. Yang, T. Qin, A. Morais, A. Harriott, S. Sakadžić, C. Ayata, B. L. Edlow, D. Y. Chung,
“A novel local regression approach to analyze functional connectivity following CSD”,
International Conference on Spreading Depolarizations, Szeged, Hungary, Oct. 2023.H. J. Freeman†, J. Li†, A. Meydan, N. Gilmore, S. B. Snider, H. Carrington, E. Selmanovic, A. Pruyser, A. Seifert, D. Hunt, E. J. Iglesias, C. L. Mac Donald, K. Dams-O’Connor, B. L. Edlow,
“Improved cortical lesion segmentation using SynthSR”,
IEEE-EMBS International Conference on Biomedical and Health Informatics, Pittsburgh, PA, Oct. 2023.Y. Liu, J. Li, J. L. Wisnowski, R. M. Leahy,
“Cortical parcellation with graph representation learning on resting-state fMRI”,
22nd International Workshop on Data Mining in Bioinformatics, Long Beach, CA, Aug. 2023.J. Mentch, J. Li, S. Ghosh,
“Identifying brain networks in a clinically rich and naturalistic dataset using tensor decomposition”,
29th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, Jul. 2023.M. D. Olchanyi, H. J. Freeman, H. C. Kinney, S. B. Snider, J. Li, J. E. Iglesias, Y. G. Bodien, C. Maffei, J. Augustinack, L. Zöllei, D. N. Greve, M. Bianciardi, B. R. Diamond, R. J. Cali, J. C. Nolan, A. Stevens, A. Yendiki, J. T. Giacino, A. Kouwe, C. Destrieux, R. D. Folkerth, B. Fischl, E. N. Brown, B. L. Edlow,
“Mapping the human default arousal network connectome”,
29th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, Jul. 2023.
2022
Y. Liu, J. Li, J. L. Wisnowski, R. M. Leahy,
“Functional parcellation of the cerebral cortex based on brain network identification using resting-state fMRI”,
51st Annual Meeting of the Society for Neuroscience, San Diego, CA, Nov. 2022.O. Grinenko†, T. Aung†, J. Li, J. C. Mosher, P. Chauvel, J. Gonzalez-Martinez,
“Stereo-electroencephalography guided laser ablation in neocortical epilepsy: Electrophysiological biomarker and seizure outcome”,
76th Annual Meeting of the American Epilepsy Society, Nashville, TN, Dec. 2022.- M. Daneshzand, A. Nummenmaa, J. Li, L. Vendramini, J. Stockmann, T. Chou, D. Dougherty, B. Edlow, B. Guerin,
“Simulation and visualization tool for subject-specific tFUS neuronavigation”,
21th Annual International Symposium on Therapeutic Ultrasound, Toronto, Canada, Jun. 2022.Abstract
Objectives: To provide an open-source, user-friendly MATLAB-based application for simulation and planning of transcranial Focused Ultrasound (tFUS) human studies as well as real-time tFUS neuronavigation. Methods: We use mSOUND, a fast angular spectrum method that models nonlinear ultrasound propagation in heterogeneous media (e.g., skull). The pipeline consists of 1) generation of a pseudo-CT image from a T1w-MRI image; 2) computation of tFUS acoustic beams of the transducer at hundreds of locations on the scalp; 3) a tool for visualization of the beams at the modeled transducer locations, and 4) real-time neuronavigation for visualization of the tFUS beam when moving the transducer. Results: Pre-processing steps 1) and 2) take ~12 hours for simulation of a 650kHz focused transducer at ~1000 locations on the subject’ scalp with mSOUND. For each beam solution, 3D rendered surfaces of the intensity distribution are saved, along with the average acoustic energy deposition for various deep brain nuclei, evaluated using FreeSurfer. These data are accessed for rapid visualization of different beam solutions for tFUS planning (step 3) and real-time neuronavigation (step 4). Using a navigation system with optical tracking, TMS Navigator (Localite, Germany), an overall frame rate of 2 Hz for MATLAB-based beam calculations and visualization was achieved. Conclusions: The proposed tool allows subject-specific, simulation-based planning and real-time visualization of the acoustic beam created by curved ultrasound transducers at hundreds of locations on the scalp. We are currently evaluating the impact of skull-induced beam deformations on tFUS navigation compared to line of sight targeting approach.
J. Li, M. K. Cambareri, B. Guerin, D. D. Dougherty, A. V. Dalca, B. Fischl, A. Horn, B. L. Edlow,
“Towards clinical translation of default mode subcortical targeting for therapeutic neuromodulation”,
28th Annual Meeting of the Organization for Human Brain Mapping, Glasgow, Scotland, Jun. 2022.- M. K. Cambareri, J. Li, L. D. Lewis, B. L. Edlow,
“Exploration of subcortical functional connectivity for therapeutic neuromodulation targeting”,
28th Annual Meeting of the Organization for Human Brain Mapping, Glasgow, Scotland, Jun. 2022.
2021
B. Guerin, M. Daneshzand, J. Stockmann, J. Li, B. L. Edlow, D. D. Dougherty, A. Nummenma,
“Precomputation of hundreds of transducer positions for real-time stimulation-based neuronavigation of neuromodulation using tFUS”,
2nd Focused Ultrasound Neuromodulation Symposium, Virtual Conference, Sept. 2021.J. Li, W. H. Curley, B. Guerin, D. D. Dougherty, A. V. Dalca, A. Horn, B. L. Edlow,
“The subcortical connectome of the default mode network”,
NIH Common Fund’s 2021 High-Risk, High-Reward Research Symposium, Jun. 2021.R. Setton, L. Mwilambwe-Tshilobo, M. Girn, A. Lockrow, G. Baracchini, A. Lowe, B. Cassidy, J. Li, D. Bzdock, R. Leahy, T. Ge, D. Margulies, B. Misic, B. Bernhardt, W. Stevens, F. De Brigard, P. Kundu, G. Turner, N. Spreng,
“Functional architecture of the aging brain”,
27th Annual Meeting of the Organization for Human Brain Mapping, Seoul, Korea, Jun. 2021.Y. Liu, J. Li, J. L. Wisnowski, A. A. Joshi, R. M. Leahy,
“Brain network decomposition for naturalistic stimulus paradigm”,
27th Annual Meeting of the Organization for Human Brain Mapping, Seoul, Korea, Jun. 2021.J. Li, W. H. Curley, B. Guerin, D. D. Dougherty, A. V. Dalca, B. L. Edlow,
“Mapping subcortical functional connectome of the default mode network for targeted neuromodulation”,
27th Annual Meeting of the Organization for Human Brain Mapping, Seoul, Korea, Jun. 2021.
2020
- H. Shaker, J. Li, M. Kobayashi, J. Bulacio, I. Najm, P. Chauvel,
“Functional significance of epileptogenic fast activity: A study of motor cortex seizures”,
74th Annual Meeting of the American Epilepsy Society, Seattle, WA, Dec. 2020.Abstract
Rationale: High-frequency activities (HFAs) in human epilepsies have been subject to many studies for a decade. Most of them have been dedicated to interictal high-frequency oscillations (HFOs) with emphasis on their correlation with the epileptogenic zone localization. Few of them have addressed the question of HFAs as an ictal pattern and even less have analyzed their relation to clinical semiology. The present study has been designed to analyze the electrophysiological effect of a narrow-band fast activity onto the efferent volleys of the motor cortex during locally generated epileptic seizures. Method: High-frequency activities (HFAs) in human epilepsies have been subject to many studies for a decade. Most of them have been dedicated to interictal high-frequency oscillations (HFOs) with emphasis on their correlation with the epileptogenic zone localization. Few of them have addressed the question of HFAs as an ictal pattern and even less have analyzed their relation to clinical semiology. The present study has been designed to analyze the electrophysiological effect of a narrow-band fast activity onto the efferent volleys of the motor cortex during locally generated epileptic seizures. Results5 patients (3 male and 2 females, mean age 22.4 years old) with 157 analyzable seizures fulfilled the selection criteria. Patient #1 did not present any clinical motor signs during HFA. The first motor sign corresponded to the onset of beta rhythm sustained activity (< 30 Hz). The same was observed in patient #2: the earliest clonic movement occurred simultaneously with a subsequent beta activity. Patient #3 was a child who was crying due to inability to move her left hand in the beginning of her seizures. Her arm was actually atonic as long as the motor cortex discharge kept in HFA range. Clonic movements appeared in the same arm when HFA vanished and alpha/beta activity emerged. Patient #4 presented with multiple clusters of brief atonic and tonic facial motor signs. Two distinct frequency patterns correlated with the two states. A high-gamma activity was associated to the atonic facial seizures and a beta/low gamma activity to the facial tonic seizures. An ictal rhythm of low gamma/beta activity (18-35 Hz) without any HFA correlated with tonic left arm and shoulder motor signs in patient #5. A quantitative analysis using time-frequency plots confirmed an epileptogenic zone fingerprint in all patients. Latency of motor sign onset with respect to the onset and duration of fast activity was analyzed. A significant correlation ( with an uncorrected p-value of ) between the two measures was observed, indicating that the longer the HFA the longer the latency of motor signs. Conclusion: Epileptogenic frequency patterns have a pathophysiological significance. This study on primary motor cortex seizures allowed a direct measure of the cortical output. HFAs were showed to have an opposite functional effect according to their frequency range. High gamma fast activity was associated with an inhibition of the motor cortex output. Tonic ictal discharges in the beta/low gamma range were the frequency pattern associated with tonic motor signs.
R. Setton, L. Mwilambwe-Tshilobo, G. Baracchini, M. Girn, A. Lockrow, P. Kundu, J. Li, T. Ge, R. M. Leahy, G. Turner, N. Spreng,
“ME-fMRI connectivity associations with behavior using group and individualized parcellation schemes”,
26th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, Jun. 2020.- A. A. Joshi, S. Choi, J. Li, H. Akrami, R. M. Leahy,
“A novel approach for group fMRI studies using BrainSync transform and pair-wise statistics”,
26th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, Jun. 2020.
2019
S. Choi, A. A. Joshi, S. H. O’Neil, X. Miao, J. Li, J. P. Haldar, T. Coates, R. M. Leahy, J. C. Wood,
“Exploring anemia’s impact on brain microstructure, volume, functional connectivity, iron and cognitive performance”,
61st Annual Meeting of the American Society of Hematology, Orlando, FL, Dec. 2019.M. Kobayashi, O. Grinenko, J. Li, B. Krishnan, D. R. Nair, P. Chauvel,
“Association of ictal slow shift with the “fingerprint” of epileptogenic zone”,
73rd Annual Meeting of the American Epilepsy Society, Baltimore, MD, Dec. 2019.J. Li, J. C. Mosher, J. Gonzalez-Martinez, D. R. Nair, R. M. Leahy,
“Fingerprint propagation and the epileptogenic zone localization using cortico-cortical evoked potentials”,
73rd Annual Meeting of the American Epilepsy Society, Baltimore, MD, Dec. 2019.H. Akrami, A. A. Joshi, J. Li, R. M. Leahy,
“Traumatic brain injury lesion detection using a variational autoencoder”,
73rd Annual Meeting of the American Epilepsy Society, Baltimore, MD, Dec. 2019.A. A. Joshi, H. Akrami, J. Li, R. M. Leahy,
“A matched filter decomposition of task fMRI for extraction of dynamical components”,
25th Annual Meeting of the Organization for Human Brain Mapping, Rome, Italy, Jun. 2019.S. Choi, A. A. Joshi, C. Vu, J. Li, S. O’Neil, J. C. Wood, R. M. Leahy,
“Alterations of brain connectivity in anemic subjects using fMRI under hypoxic and hyperoxic states”,
25th Annual Meeting of the Organization for Human Brain Mapping, Rome, Italy, Jun. 2019.
2018
O. Grinenko, J. Li, J. C. Mosher, J. C. Bulacio, J. Gonzalez-Martinez, I. Najm, P. Chauvel, R. M. Leahy,
“In search of biomarkers for the epileptogenic zone: A machine learning approach”,
72nd Annual Meeting of the American Epilepsy Society, New Orleans, LA, Dec. 2018.J. Li, J. L. Wisnowski, A. A. Joshi, R. M. Leahy,
“Identifying brain networks using tensor decomposition of multiple subject asynchronous task fMRI”,
24th Annual Meeting of the Organization for Human Brain Mapping, Singapore, Republic of Singapore, Jun. 2018.H. Akrami, A. A. Joshi, J. Li, R. M. Leahy,
“Average template for comparison of resting fMRI based on group synchronization of their time series”,
24th Annual Meeting of the Organization for Human Brain Mapping, Singapore, Republic of Singapore, Jun. 2018.A. A. Joshi, D. McCoy, M. Chong, J. Li, S. Choi, D. Shattuck, R. M. Leahy,
“BFP: BrainSuite fMRI pipeline”,
24th Annual Meeting of the Organization for Human Brain Mapping, Singapore, Republic of Singapore, Jun. 2018.
2017
J. Li, S. E. Luczak, I. G. Rosen,
“On the modeling and deconvolution of blood or breath alcohol concentration (BrAC/BAC) from biosensor-measured transdermal alcohol concentration (TAC)”,
40th Annual Meeting of the Research Society on Alcoholism, Denver, CO, Jun. 2017.J. Li, S. Choi, R. M. Leahy,
“Global PDF-based non-local means filtering of resting fMRI data”,
23rd Annual Meeting of the Organization for Human Brain Mapping, Vancouver, Canada, Jun. 2017.