Benjamin Brinkmann | Mayo Clinic (original) (raw)

Papers by Benjamin Brinkmann

Brain : a journal of neurology, 2017

There exist significant clinical and basic research needs for accurate, automated seizure detecti... more There exist significant clinical and basic research needs for accurate, automated seizure detection algorithms. These algorithms have translational potential in responsive neurostimulation devices and in automatic parsing of continuous intracranial electroencephalography data. An important barrier to developing accurate, validated algorithms for seizure detection is limited access to high-quality, expertly annotated seizure data from prolonged recordings. To overcome this, we hosted a kaggle.com competition to crowdsource the development of seizure detection algorithms using intracranial electroencephalography from canines and humans with epilepsy. The top three performing algorithms from the contest were then validated on out-of-sample patient data including standard clinical data and continuous ambulatory human data obtained over several years using the implantable NeuroVista seizure advisory system. Two hundred teams of data scientists from all over the world participated in the ...

ABSTRACT Without Abstract

ABSTRACT Thesis (Ph.D.) -- Biomedical Imaging Resource -- Mayo Graduate School, [1999]. Includes ... more ABSTRACT Thesis (Ph.D.) -- Biomedical Imaging Resource -- Mayo Graduate School, [1999]. Includes bibliographical references (leaves 127-137) and index.

Medical Imaging 1997: Physiology and Function from Multidimensional Images, 1997

ABSTRACT Advances in neuroimaging have enhanced the clinician's ability to localize the e... more ABSTRACT Advances in neuroimaging have enhanced the clinician's ability to localize the epileptogenic zone in focal epilepsy, but 20-50 percent of these cases still remain unlocalized. Many sophisticated modalities have been used to study epilepsy, but scalp electrode recorded electroencephalography is particularly useful due to its noninvasive nature and excellent temporal resolution. This study is aimed at specific locations of scalp electrode EEG information for correlation with anatomical structures in the brain. 3D position localizing devices commonly used in virtual reality systems are used to digitize the coordinates of scalp electrodes in a standard clinical configuration. The electrode coordinates are registered with a high- resolution MRI dataset using a robust surface matching algorithm. Volume rendering can then be used to visualize the electrodes and electrode potentials interpolated over the scalp. The accuracy of the coordinate registration is assessed quantitatively with a realistic head phantom. Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Abstract Text Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints

Lecture Notes in Computer Science, 1998

... Epilepsia 1997;38 (Suppl. 3):9. 6. Berkovic SF, Newton M, Chiron C, Dulac O. Single photon em... more ... Epilepsia 1997;38 (Suppl. 3):9. 6. Berkovic SF, Newton M, Chiron C, Dulac O. Single photon emission tomography. ... 21(12):1927-32. 9. Hanson DP, Robb RA, Aharon S, Augustine KE, Cameron BM, Camp JJ, Karwoski RA, Larson AG, Stacy MC, Workman EL. ...

PloS one, 2015

Management of drug resistant focal epilepsy would be greatly assisted by a reliable warning syste... more Management of drug resistant focal epilepsy would be greatly assisted by a reliable warning system capable of alerting patients prior to seizures to allow the patient to adjust activities or medication. Such a system requires successful identification of a preictal, or seizure-prone state. Identification of preictal states in continuous long- duration intracranial electroencephalographic (iEEG) recordings of dogs with naturally occurring epilepsy was investigated using a support vector machine (SVM) algorithm. The dogs studied were implanted with a 16-channel ambulatory iEEG recording device with average channel reference for a mean (st. dev.) of 380.4 (+87.5) days producing 220.2 (+104.1) days of intracranial EEG recorded at 400 Hz for analysis. The iEEG records had 51.6 (+52.8) seizures identified, of which 35.8 (+30.4) seizures were preceded by more than 4 hours of seizure-free data. Recorded iEEG data were stratified into 11 contiguous, non-overlapping frequency bands and binned...

Medical Imaging 1996: Image Processing, 1996

ABSTRACT Grayscale inhomogeneities in magnetic resonance (MR) images cause significant problems i... more ABSTRACT Grayscale inhomogeneities in magnetic resonance (MR) images cause significant problems in automated quantitative image analysis. Removal of such inhomogeneities is a difficult task, but it has been investigated by a number of different authors recently. The most common methods used involve some type of homomorphic filtering to create a smoothed version of the original image, which is then used as an estimate of the bias field to be removed from the image. Many investigators have implemented variations of this technique and have demonstrated their usefulness for a wide range of applications, but no investigator has yet attempted a systematic, quantitative study to describe the effects these algorithms have on images. This study introduces a quantitative paradigm for evaluating inhomogeneity correction algorithms by their performance on a constructed simulation image with different bias fields applied. We find that mean filter algorithms are more successful than median filter algorithms, and that larger kernel sizes than what are currently reported in the literature offer significant improvements in post-correction image quality.

Nuclear medicine communications, 2000

Subtraction ictal SPET co-registered to MRI (SISCOM) has been shown to aid epileptogenic localiza... more Subtraction ictal SPET co-registered to MRI (SISCOM) has been shown to aid epileptogenic localization and improve surgical outcome in partial epilepsy patients. This paper reports a method of identifying significant areas of epileptogenic activation in the SISCOM subtraction image, taking into account normal variation between sequential 99Tcm-ethyl cysteinate diethylester SPET scans of single individuals, and attempts to assess the clinical value of statistical mapping in subtraction SPET. Non-linear inter-subject registration is used to combine a group of subtraction images into a common anatomical framework. A map of the pixel intensity standard deviation values in the subtraction images is created, and this map is non-linearly registered to a patient's SISCOM subtraction image. Pixels in the patient subtraction image were then evaluated based upon the statistical characteristics of corresponding pixels in the atlas. SISCOM images created with the voxel variance method were ra...

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2014

In the present study, we developed a method for the purpose of localizing epilepsy related hemody... more In the present study, we developed a method for the purpose of localizing epilepsy related hemodynamic foci for patients suffering intractable focal epilepsy using resting state fMRI alone. We studied two groups of subjects: five patients with intractable focal epilepsy, and ten healthy volunteers performing motor tasks. Spatial independent component analysis (ICA) was performed on the fMRI alone data and a set of independent component (IC) selection criteria was developed to identify epilepsy related ICs. The method was then evaluated in the healthy group with motor tasks. In all five surgery patients, there was at least one identified IC concordant with surgical resection. In the motor task study of healthy subjects, our method revealed components with concordant spatial and temporal features as expected from the unilateral motor tasks. These results suggest the lateralization and localization value of fMRI alone in presurgical evaluation for patients with intractable unilateral f...

Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology, 2015

The aim was to develop a method for the purpose of localizing epilepsy related hemodynamic foci f... more The aim was to develop a method for the purpose of localizing epilepsy related hemodynamic foci for patients suffering intractable focal epilepsy using task-free fMRI alone. We studied three groups of subjects: patients with intractable focal epilepsy, healthy volunteers performing motor tasks, and healthy volunteers in resting state. We performed spatial independent component analysis (ICA) on the fMRI alone data and developed a set of IC selection criteria to identify epilepsy related ICs. The method was then tested in the two healthy groups. In seven out of the nine surgery patients, identified ICs were concordant with surgical resection. Our results were also consistent with presurgical evaluation of the remaining one patient without surgery and may explain why she was not suitable for resection treatment. In the motor task study of ten healthy subjects, our method revealed components with concordant spatial and temporal features as expected from the unilateral motor tasks. In t...

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2012

Epilepsy is a common neurological disease that affects about 50 million people worldwide. Extrate... more Epilepsy is a common neurological disease that affects about 50 million people worldwide. Extratemporal lobe epilepsy, which represents an important type of epilepsy, may involve seizure activity in various lobes and the surgical treatment in these patients tends to have less favorable surgical outcome. Noninvasive seizure imaging in drug-resistant patients is of vital importance to image the seizure onset zones (SOZs) and understand the mechanisms for an improved treatment plan. In this study, we directly imaged the seizure sources in 8 extratemporal lobe partial epilepsy patients from noninvasive EEG. The surgically resected regions and SOZs identified from intracranial EEG (iEEG) recordings were used to evaluate the source imaging results. All of the eight patients underwent resective surgery and the estimated seizure sources were co-located with the resection zone. Seven of the patients had iEEG recordings available and the source imaging results were concordant with the SOZs ma...

2013 6th International IEEE/EMBS Conference on Neural Engineering (NER), 2013

ABSTRACT The need for sharing and analyzing large-scale data sets in scientific research has incr... more ABSTRACT The need for sharing and analyzing large-scale data sets in scientific research has increased significantly over the last decade. Despite multiple efforts, there is currently no single platform that is widely used to search for, share, and perform custom data analysis over large numbers of TB-scale datasets using cloud technologies. We present a cloud-based portal and data integration/access platform to fulfill this need. The IEEG-Portal is being developed as a means to share and collaborate on projects containing large EEG datasets. It currently contains over 75 de-identified intracranial EEG datasets as well as imaging and associated meta-information, and a variety of datasets from animals. The IEEG-Portal is modular by design, which results in a highly extensible platform for neural data analysis on the cloud. In this paper, we highlight the current state of the portal infrastructure; its capabilities for fostering collaborative research and data-validation, and the challenges that are inherent to sharing and analyzing datasets using a global collaborative cloud-based platform.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2011

Electroencephalogram (EEG) is an important component of the pre-surgical evaluation in the treatm... more Electroencephalogram (EEG) is an important component of the pre-surgical evaluation in the treatment of medically intractable epilepsy. However, clinical EEG uses 19 to 32 electrodes that significantly limits its localization ability. Recent development of dense-array recording techniques has suggested that increased spatial sampling rate improves the accuracy of source localization. In the current study, we proposed a 76-channel EEG system for the long-term monitoring of epilepsy patients, and proposed a dynamic seizure imaging (DSI) technique to image the ictal rhythmic activity that may evolve through time, space and frequency. We tested the system in a cohort of 8 patients and our results show that the DSI estimated the seizure activity in good correlation with intracranial recordings, successful surgery outcomes and other clinical evidence. The proposed dense-array recording and DSI imaging approach enable a non-invasive but quantitative imaging of continuous seizure activity. ...

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2009

Continuous, long-term (up to 10 days) electrophysiological monitoring using hybrid intracranial e... more Continuous, long-term (up to 10 days) electrophysiological monitoring using hybrid intracranial electrodes is an emerging tool for presurgical epilepsy evaluation and fundamental investigations of seizure generation. Detection of high-frequency oscillations and microseizures could provide valuable insights into causes and therapies for the treatment of epilepsy, but requires high spatial and temporal resolution. Our group is currently using hybrid arrays composed of up to 320 micro- and clinical macroelectrode arrays sampled at 32 kHz per channel with 18-bits of A/D resolution. Such recordings produce approximately 3 terabytes of data per day. Existing file formats have limited data compression capabilities, and do not offer mechanisms for protecting patient identifying information or detecting data corruption during transmission or storage. We present a novel file format that employs range encoding to provide a high degree of data compression, a three-tiered 128-bit encryption syst...

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2009

The increasing use of high-frequency (kHz), long-duration (days) intracranial monitoring from mul... more The increasing use of high-frequency (kHz), long-duration (days) intracranial monitoring from multiple electrodes during pre-surgical evaluation for epilepsy produces large amounts of data that are challenging to store and maintain. Descriptive metadata and clinical annotations of these large data sets also pose challenges to simple, often manual, methods of data analysis. The problems of reliable communication of metadata and annotations between programs, the maintenance of the meanings within that information over long time periods, and the flexibility to re-sort data for analysis place differing demands on data structures and algorithms. Solutions to these individual problem domains (communication, storage and analysis) can be configured to provide easy translation and clarity across the domains. The Multi-scale Annotation Format (MAF) provides an integrated metadata and annotation environment that maximizes code reuse, minimizes error probability and encourages future changes by...

Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 1999

This study reports quantitative measurements of the accuracy of two popular voxel-based registrat... more This study reports quantitative measurements of the accuracy of two popular voxel-based registration algorithms--Woods' automated image registration algorithm and mutual information correlation--and compares these with conventional surface matching (SM) registration. The registration algorithms were compared (15 different matches each) for (a) three-dimensional brain phantom images, (b) an ictal SPECT image from a patient with partial epilepsy matched to itself after modification to simulate changes in the cerebral blood flow pattern and (c) ictal/interictal SPECT images from 15 patients with partial epilepsy. Blinded visual ranking and localization of the subtraction images derived from the patient images were also performed. Both voxel-based registration methods were more accurate than SM registration (P < 0.0005). Automated image registration algorithm was more accurate than mutual information correlation for the computer-simulated ictal/interictal images and the patient i...

Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 1999

The acquisition of multiple radiotracer studies at different time points during a neurological ev... more The acquisition of multiple radiotracer studies at different time points during a neurological event permits the study of different functional activation states in humans. Peri-ictal SPECT is a promising technique for localizing the epileptogenic zone and would be enhanced by the ability to acquire sequentially coregistered ictal and postictal SPECT images of a single seizure. This study was designed to develop and validate an accurate method for the simultaneous acquisition of 99mTc and 123I SPECT images of the brain. A multicompartment, transaxial Hoffman brain-slice phantom was filled with 99mTc, 123I or a 3:1 mixture of the two isotopes. Planar and SPECT images were acquired by a dual-head gamma camera system equipped with parallel and fanbeam collimators, respectively. Thirty-two energy windows (2 keV width) were acquired over the energy range 120-184 keV. From the planar data, the signal-to-noise characteristics and crosstalk were measured for each energy window and used to de...

American journal of physiology. Gastrointestinal and liver physiology, 2002

Glucagon-like peptide-1 (GLP-1) relaxes the stomach during fasting but decreases hunger and food ... more Glucagon-like peptide-1 (GLP-1) relaxes the stomach during fasting but decreases hunger and food consumption and retards gastric emptying. The interrelationships between volume, emptying, and postprandial symptoms in response to GLP-1 are unclear. We performed, in healthy human volunteers, a placebo-controlled study of the effects of intravenous GLP-1 on gastric volume using (99m)Tc-single photon emission computed tomography imaging, gastric emptying of a nutrient liquid meal (Ensure) using scintigraphy, maximum tolerated volume (MTV) of Ensure, and postprandial symptoms 30 min after MTV. The role of vagal cholinergic function in the effects of GLP-1 was assessed by human pancreatic polypeptide (HPP) response to the Ensure meal. GLP-1 increased fasting and postprandial gastric volumes and retarded gastric emptying; MTV and postprandial symptoms were not different compared with controls. Effects on postprandial gastric function were associated with reduced postprandial HPP levels. GL...

Neurology, 2015

Objective: To investigate the generation, spectral characteristics, and potential clinical signif... more Objective: To investigate the generation, spectral characteristics, and potential clinical significance of brain activity preceding interictal epileptiform spike discharges (IEDs) recorded with intracranial EEG.