This work was made possible by grants supported by the US Army Research Office (W911NF-07-1-0415 (GS), W911NF-08-1-0216 (GS)) and the NIH/NIBIB (EB006356 (GS) and EB00856 (JRW and GS)). The authors thank Sean Austin for the SigfriedSigProcLAVA module, and Griffin Milsap for related technical assistance.

1. Electrode Localization
<ol>
	<li>Collect a pre-operative T1-weighted structural MRI (1.5T or 3T) of the patient's head: 256 x 256 pixels per slice, full field of view, no interpolation, 1 mm slice width, preferably sagittal cross-sections.</li>
	<li>Observe the surgical implantation of the grids and strips. Collect digital photographs of the electrodes in situ, and the neurosurgeon's notes on the locations of the implanted grids and strips.</li>
	<li>Collect the post-operative skull X-ray images and brain CT scans at high resolution (1 mm slice width, skin to skin, no angle).</li>
	<li>Create a three-dimensional cortical model of the patient's brain using the pre-operative MRI, and co-register it with the post-grid implantation CT images. We use the CURRY software package for this purpose, and export the 3D cortical structure and electrode coordinates in MATLAB format. From MATLAB, we export a movie that shows the electrodes mapped onto the brain. We also map the electrode coordinates to standard Brodmann areas using an automated Talairach atlas.</li>
	<li>Review the information from the 3D model, X-ray images, photographs and notes. Finalize a numbering scheme for the electrodes, and work with the hospital technicians to ensure that the electrodes are patched into the splitter boxes following this numbering exactly. Also create a schematic layout for plotting the electrodes in two dimensions, such that all the electrode positions can be clearly distinguished without overlapping. If you are going to run SIGFRIED (see section 4), save these two-dimensional coordinates as a BCI2000 parameter fragment, in the format required by the ElectrodeLocations parameter. Finally, select two electrode locations that are likely to be electrocorticographically "silent," i.e., they are not near the presumed eloquent cortex, to use as an initial ground and reference (prepare the g.USBamps by patching the reference to the blue sockets, and ground to the yellow sockets, on the extreme right of each unit).</li>
</ol>
2. Hardware and Software Setup
<ol>
	<li>Ensure that the computer specifications are adequate for handling the processing requirements of the experiment. A multi-core processor will likely be necessary to accommodate the demands of real-time data acquisition and processing, video recording, and other necessary tasks. For recording and real-time analysis of 128 channels at 1200 Hz, we use a 3-GHz quad-core machine with 4 GB of RAM. The amplifiers should be connected to a dedicated USB controller, distinct from the controller(s) used by other bandwidth-hungry peripherals, such as external drives and cameras (this can be verified via the system's Device Manager). Finally, there must be sufficient disk space to store up to 5 MB per second of experimental data, and a system for archiving and backing it up.</li>
	<li>Set up the research equipment (amplifiers, computer, experimenter's screen, keyboard, speakers, microphone and camera) on a single trolley, which can be quickly rolled in and out of the patient's room, with only a single power cord to plug into the wall. To move the computer from room to room, use the Hibernate function before unplugging. The patient's video screen should be on a separate tray table or monitor arm. Considering that the patient is prone to seizures, make sure that all the equipment can be rolled out of the way quickly in case medical personnel need immediate access to the patient. The equipment should also be disinfected with antiseptic wipes before and after use in the patient's room.</li>
	<li>Time with the patient is limited, and all procedures need to be robust and optimized to make best use of that time. In this regard, the flexibility and robustness of BCI2000 are invaluable characteristics. Ensure that the experiments can be launched at the touch of a button. In the case of BCI2000, use a batch file to launch the right combination of BCI2000 modules automatically, with the required command-line options. The Operator and gUSBampSource modules are required, along with the appropriate SignalProcessing and Application modules for your particular experiment. Use BCI2000's Operator scripting feature to ensure that all the required parameter files are loaded automatically-including any that are specific to this patient, such as the number of electrodes and their names and positions. The purpose of this automation is to minimize the number of manual steps by the experimenter, and thus the opportunities for error. The software and its parameters need to have been finalized and tested (perhaps with an EEG subject) at least one or two weeks before implantation. It is also highly advisable to perform a "dry" run the day before the first experimental session, including all the new patient-specific parameters.</li>
</ol>
3. Experimental Session Set-up
<ol>
	<li>Choose your moment for suggesting experimental recordings to the patient, giving them notice earlier in the day, and again 15 minutes before you start. Work around visitors, meals, naps, medical procedures, and the patient's physical, emotional and cognitive state. It is important to establish a rapport with medical personnel on the floor, to help in optimizing the timing and duration of recordings.</li>
	<li>Wheel the equipment into place, connect to the power outlet, turn on the subject's video screen and connect it to the computer, and un-hibernate the computer.</li>
	<li>Launch BCI2000. With the VisualizeSource parameter enabled, press Set Config. The signal viewer opens, letting you assess the ECoG signal quality. Right-click on the viewer and set the high-pass filter to a 5 Hz cutoff. (This filter setting will only affect visualization, and not collection of data.)</li>
	<li>Check for interference from power line noise: Does activating a notch filter in the viewer (at 50 Hz or 60 Hz, depending on which country you are in) make a big difference to the signal? If so, try to reduce this by removing any unused cross-talking cables, or identifying and removing other sources of power interference. Change the electrodes used for reference and ground if necessary.</li>
	<li>If you are using an eye-tracker, calibrate it using the calibration software provided by the manufacturer. The BCI2000 source module should be compiled with the EyetrackerLogger extension included, and should be launched with the --LogEyetracker=1 flag enabled, so that eye-tracking data can be acquired in synch with the ECoG signals.</li>
	<li>To avoid distractions and interruptions, and to minimize possible signal interference, ensure that TVs, radios and mobile phones are turned off.</li>
	<li>Give precise instructions to the patient for the experiment you are about to run. Depending on the subject's task, prepared Powerpoint slides that show the task, the suggested posture, etc., can prove useful.</li>
	<li>Press Start on the Operator to start the experiment. Each time you press Start or Resume, a new file will be created to avoid overwriting previous data, and the file will be initialized with a copy of all the parameter values. Raw data will then be streamed automatically to the file, along with event markers, until you press Suspend or the experimental run finishes.</li>
	<li>Throughout the session, monitor the patient's behavior and the ECoG signals for suspected seizures, and be ready to respond to instructions from medical staff.</li>
</ol>
4. Example Experimental Session: SIGFRIED Clinical Mapping with BCI2000
<ol>
	<li>Preparation: Before the session starts, you will need to have prepared a model.ini file that contains the signal-processing settings SIGFRIED will use to build a model, and a .prm file (or separate .prm fragments) containing the BCI2000 parameters that the SigfriedSigProc module will use for real-time visualization. Two key parameters are ElectrodeLocations, specifying the 2-D layout you have chosen for this patient's particular electrodes, and ElectrodeCondition, which specifies which different tasks will be mapped under which conditions. In this example, we are using the simple StimulusPresentation module for communicating instructions to the patient, so the Stimuli parameter also needs to be adapted to the tasks we intend to run.</li>
	<li>Baseline Step: Start the gUSBampSource, DummySignalProcessing and StimulusPresentationTask modules, configured to sample ECoG activity from all grids and strips at 1200Hz, high-pass-filtered at 0.1 Hz. Instruct the subject to relax and remain motionless with eyes open. Record 6 minutes of baseline activity, under comfortable illumination in a quiet environment.</li>
	<li>Modeling Step: Start the data2model_gui tool and extract features in 5 Hz bins from 70 to 110 Hz using maximum entropy method for every 500 ms of data. Press Build Model to build a probabilistic model of the selected spectral features using Gaussian mixtures.</li>
	<li>Mapping Step: Start the gUSBampSource, SigfriedSigProcLAVA and StimulusPresentationTask modules and configure the Operator to load the probabilistic model, the cortical model, and the 2- and 3-dimensional electrode coordinates. After instructing the subject, start the mapping process. In this process, a subject will perform each task for 10 seconds at a time, on each of 5 repetitions. During each task, SIGFRIED detects task-related ECoG activity that is presented in continuously updated 2- and 3-dimensional maps of eloquent cortex. In the 2-dimensional maps, the size and redness of each circle represents its importance in this particular task. Specifically, the size of each circle is proportional to the fraction of the total signal variance in the gamma band that is accounted for by the task. This statistic is known as the coefficient of determination, or r2. It is in the range (0,1) and in the current setup a value of 0.1 can generally be considered significant. The scaling of the circles to maximum r2 values can be controlled using the sliders (see Figure 1C). In the 3-dimensional maps, the r2 values are mapped to different colors rather than circle sizes.</li>
</ol>
5. Representative Results
Figure 1 shows representative results, from one SIGFRIED mapping session in one patient. The patient was a 28-year-old right-handed female who had intractable localization-related epilepsy of left-temporal onset with secondary generalization. 120 electrocorticographic electrodes were implanted subdurally over left frontal, parietal and temporal cortex. A lateral x-ray (panel A) and an intra-operative photograph (panel B) depict the configuration of one frontal grid with 40 electrodes, one higher-density temporal grid with 68 electrodes, and three strips each of 4 electrodes. From the recorded seizures, a neurologist localized the epileptic foci and determined that it was necessary to perform surgical resection of the left temporal lobe while sparing eloquent language cortex. This was performed successfully: at 8 months post-resection the patient has been assessed as seizure free and without neurological deficits. The passive mapping procedure SIGFRIED identified cortex involved in language function by contrasting task-related changes during listening tasks. The results were presented in two interfaces: a 2-dimensional interface (panel C), which makes the layout of the electrodes clear, and a 3-dimensional anatomically-correct interface (panel D). From left to right the panels contrast listening to spoken language vs baseline (VOICE), listening to tones vs baseline (TONES), and listening to spoken language vs listening to tones (LANGUAGE). The last of these is included as a rough picture of auditory function that is specific to receptive language. The results of the VOICE condition showed good agreement with locations at which ECS disrupted receptive language function in this patient (marked as yellow circles in panel A).
<img alt="Figure 1" src="/files/ftp_upload/3993/3993fig1.jpg" /> 
Figure 1. Example results from one patient. Panel A shows a lateral x-ray. Yellow circles mark the electrodes implicated in receptive language, as subsequently identified by electrocortical stimulation mapping. Panel B is a photograph taken during implantation. Panel C shows the SIGFRIED mapping results in a schematic two-dimensional layout: the size and redness of each disc represents the significance of the involvement of each electrode in the task, relative to baseline. In panel D, the same statistic is mapped to color on a three-dimensional brain model rendered from the patient's MRI.

<ol>
	<li>Miller, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectral+Changes+in+Cortical+Surface+Potentials+during+Motor+Movement.">Spectral Changes in Cortical Surface Potentials during Motor Movement.</a> Journal of Neuroscience. 27, 2424-2424 (2007).</li><li>Chang, E. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Categorical+speech+representation+in+human+superior+temporal+gyrus.">Categorical speech representation in human superior temporal gyrus.</a> Nature Neuroscience. 13, 1428-1428 (2010).</li><li>Gunduz, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neural+correlates+of+visual-spatial+attention+in+electrocorticographic+signals+in+humans.">Neural correlates of visual-spatial attention in electrocorticographic signals in humans.</a> Frontiers in Human Neuroscience. 5, (2011).</li><li>Pei, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatiotemporal+dynamics+of+electrocorticographic+high+gamma+activity+during+overt+and+covert+word+repetition.">Spatiotemporal dynamics of electrocorticographic high gamma activity during overt and covert word repetition.</a> NeuroImage. 54, 2960 (2010).</li><li>Crone, N. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-frequency+gamma+oscillations+and+human+brain+mapping+with+electrocorticography.">High-frequency gamma oscillations and human brain mapping with electrocorticography.</a> Progress in Brain Research. 159, 275 (2006).</li><li>Brunner, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+communication+with+a+"P300"+matrix+speller+using+electrocorticographic+signals+(ECoG).">Rapid communication with a "P300" matrix speller using electrocorticographic signals (ECoG).</a> Frontiers in Neuroprosthetics. 5, (2010).</li><li>Leuthardt, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+brain-computer+interface+using+electrocorticographic+signals+in+humans.">A brain-computer interface using electrocorticographic signals in humans.</a> Journal of Neural Engineering. 1, (2004).</li><li>Schalk, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BCI2000:+A+General-Purpose+Brain-Computer+Interface+(BCI)+System.">BCI2000: A General-Purpose Brain-Computer Interface (BCI) System.</a> IEEE Transactions in Biomedical Engineering. 51, 1034 (2004).</li><li>Schalk, G., Mellinger, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> A Practical Guide to Brain-Computer Interfacing with BCI2000. , (2010).</li><li>Brunner, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+practical+procedure+for+real-time+functional+mapping+of+eloquent+cortex+using+electrocorticographic+signals+in+humans.">A practical procedure for real-time functional mapping of eloquent cortex using electrocorticographic signals in humans.</a> Epilepsy and Behavior. 15, 278 (2009).</li></ol>

No conflicts of interest declared.

Gathering ECoG data for research requires close cooperation between clinicians and researchers, with a highly multi-disciplinary team solving problems in clinical neurology, neurosurgery, basic neuroscience, computer science and electrical engineering. The reward is that ECoG signals, and in particular amplitudes in the high gamma frequency range (70-110Hz), are highly valuable. Not only do they provide scientific insight into the neural correlates of cognitive, sensory and motor processes1-4 at a both high s...

<ol>
 <li>8 x 16-channel g.USBamp amplifiers ( <a href="http://gtec.at" target="_blank">http://gtec.at</a> )</li>
 <li>2 x 64-channel break-out box (splitter head-box)</li>
 <li>2 x Connection cable from splitter to clinical system</li>
 <li>2 x Connection cable from splitter to four g.USBamps</li>
 <li>2 x Four-way power adapter for four g.USBamps</li>
 <li>2 x Four-way sync adapter to synchronize four g.USBamps</li>
 <li>1 x Sync cable to synchronize two sets of four g.USBamps</li>
 <li>1 x Potential-equalization clamp + cable for g.USBamp</li>
 <li>18 x Touchproof jumper cables</li>
 <li>2 x Four-way USB 2.0 hubs</li>
 <li>Power strip</li>
 <li>Laptop or desktop computer (see section 2.1)</li>
 <li>Secure, moveable cart for all of the above</li>
 <li>Eyetracker (or ordinary LCD monitor) for patient</li>
 <li>Moveable tray table for the patient monitor</li>
 <li>Other peripherals (joysticks etc) for patient behavioral responses</li>
 <li>BCI2000 software</li>
 <li>CURRY software</li>
 <li>MATLAB software</li>
</ol>

recording human electrocorticographic (ecog) signals for neuroscientific research and real-time functional cortical mapping

Neuroimaging studies of human cognitive, sensory, and motor processes are usually based on noninvasive techniques such as electroencephalography (EEG), magnetoencephalography or functional magnetic-resonance imaging. These techniques have either inherently low temporal or low spatial resolution, and suffer from low signal-to-noise ratio and/or poor high-frequency sensitivity. Thus, they are suboptimal for exploring the short-lived spatio-temporal dynamics of many of the underlying brain processes. In contrast, the invasive technique of electrocorticography (ECoG) provides brain signals that have an exceptionally high signal-to-noise ratio, less susceptibility to artifacts than EEG, and a high spatial and temporal resolution (i.e., &lt;1 cm/&lt;1 millisecond, respectively). ECoG involves measurement of electrical brain signals using electrodes that are implanted subdurally on the surface of the brain. Recent studies have shown that ECoG amplitudes in certain frequency bands carry substantial information about task-related activity, such as motor execution and planning1, auditory processing2 and visual-spatial attention3. Most of this information is captured in the high gamma range (around 70-110 Hz). Thus, gamma activity has been proposed as a robust and general indicator of local cortical function1-5. ECoG can also reveal functional connectivity and resolve finer task-related spatial-temporal dynamics, thereby advancing our understanding of large-scale cortical processes. It has especially proven useful for advancing brain-computer interfacing (BCI) technology for decoding a user's intentions to enhance or improve communication6 and control7. Nevertheless, human ECoG data are often hard to obtain because of the risks and limitations of the invasive procedures involved, and the need to record within the constraints of clinical settings. Still, clinical monitoring to localize epileptic foci offers a unique and valuable opportunity to collect human ECoG data. We describe our methods for collecting recording ECoG, and demonstrate how to use these signals for important real-time applications such as clinical mapping and brain-computer interfacing. Our example uses the BCI2000 software platform8,9 and the SIGFRIED10 method, an application for real-time mapping of brain functions. This procedure yields information that clinicians can subsequently use to guide the complex and laborious process of functional mapping by electrical stimulation.
Prerequisites and Planning:
Patients with drug-resistant partial epilepsy may be candidates for resective surgery of an epileptic focus to minimize the frequency of seizures. Prior to resection, the patients undergo monitoring using subdural electrodes for two purposes: first, to localize the epileptic focus, and second, to identify nearby critical brain areas (i.e., eloquent cortex) where resection could result in long-term functional deficits. To implant electrodes, a craniotomy is performed to open the skull. Then, electrode grids and/or strips are placed on the cortex, usually beneath the dura. A typical grid has a set of 8 x 8 platinum-iridium electrodes of 4 mm diameter (2.3 mm exposed surface) embedded in silicon with an inter-electrode distance of 1cm. A strip typically contains 4 or 6 such electrodes in a single line. The locations for these grids/strips are planned by a team of neurologists and neurosurgeons, and are based on previous EEG monitoring, on a structural MRI of the patient's brain, and on relevant factors of the patient's history. Continuous recording over a period of 5-12 days serves to localize epileptic foci, and electrical stimulation via the implanted electrodes allows clinicians to map eloquent cortex. At the end of the monitoring period, explantation of the electrodes and therapeutic resection are performed together in one procedure.
In addition to its primary clinical purpose, invasive monitoring also provides a unique opportunity to acquire human ECoG data for neuroscientific research. The decision to include a prospective patient in the research is based on the planned location of their electrodes, on the patient's performance scores on neuropsychological assessments, and on their informed consent, which is predicated on their understanding that participation in research is optional and is not related to their treatment. As with all research involving human subjects, the research protocol must be approved by the hospital's institutional review board. The decision to perform individual experimental tasks is made day-by-day, and is contingent on the patient's endurance and willingness to participate. Some or all of the experiments may be prevented by problems with the clinical state of the patient, such as post-operative facial swelling, temporary aphasia, frequent seizures, post-ictal fatigue and confusion, and more general pain or discomfort.
At the Epilepsy Monitoring Unit at Albany Medical Center in Albany, New York, clinical monitoring is implemented around the clock using a 192-channel Nihon-Kohden Neurofax monitoring system. Research recordings are made in collaboration with the Wadsworth Center of the New York State Department of Health in Albany. Signals from the ECoG electrodes are fed simultaneously to the research and the clinical systems via splitter connectors. To ensure that the clinical and research systems do not interfere with each other, the two systems typically use separate grounds. In fact, an epidural strip of electrodes is sometimes implanted to provide a ground for the clinical system. Whether research or clinical recording system, the grounding electrode is chosen to be distant from the predicted epileptic focus and from cortical areas of interest for the research. Our research system consists of eight synchronized 16-channel g.USBamp amplifier/digitizer units (g.tec, Graz, Austria). These were chosen because they are safety-rated and FDA-approved for invasive recordings, they have a very low noise-floor in the high-frequency range in which the signals of interest are found, and they come with an SDK that allows them to be integrated with custom-written research software. In order to capture the high-gamma signal accurately, we acquire signals at 1200Hz sampling rate-considerably higher than that of the typical EEG experiment or that of many clinical monitoring systems. A built-in low-pass filter automatically prevents aliasing of signals higher than the digitizer can capture. The patient's eye gaze is tracked using a monitor with a built-in Tobii T-60 eye-tracking system (Tobii Tech., Stockholm, Sweden). Additional accessories such as joystick, bluetooth Wiimote (Nintendo Co.), data-glove (5th Dimension Technologies), keyboard, microphone, headphones, or video camera are connected depending on the requirements of the particular experiment.
Data collection, stimulus presentation, synchronization with the different input/output accessories, and real-time analysis and visualization are accomplished using our BCI2000 software8,9. BCI2000 is a freely available general-purpose software system for real-time biosignal data acquisition, processing and feedback. It includes an array of pre-built modules that can be flexibly configured for many different purposes, and that can be extended by researchers' own code in C++, MATLAB or Python. BCI2000 consists of four modules that communicate with each other via a network-capable protocol: a Source module that handles the acquisition of brain signals from one of 19 different hardware systems from different manufacturers; a Signal Processing module that extracts relevant ECoG features and translates them into output signals; an Application module that delivers stimuli and feedback to the subject; and the Operator module that provides a graphical interface to the investigator.
A number of different experiments may be conducted with any given patient. The priority of experiments will be determined by the location of the particular patient's electrodes. However, we usually begin our experimentation using the SIGFRIED (SIGnal modeling For Realtime Identification and Event Detection) mapping method, which detects and displays significant task-related activity in real time. The resulting functional map allows us to further tailor subsequent experimental protocols and may also prove as a useful starting point for traditional mapping by electrocortical stimulation (ECS).
Although ECS mapping remains the gold standard for predicting the clinical outcome of resection, the process of ECS mapping is time consuming and also has other problems, such as after-discharges or seizures. Thus, a passive functional mapping technique may prove valuable in providing an initial estimate of the locus of eloquent cortex, which may then be confirmed and refined by ECS. The results from our passive SIGFRIED mapping technique have been shown to exhibit substantial concurrence with the results derived using ECS mapping10.
The protocol described in this paper establishes a general methodology for gathering human ECoG data, before proceeding to illustrate how experiments can be initiated using the BCI2000 software platform. Finally, as a specific example, we describe how to perform passive functional mapping using the BCI2000-based SIGFRIED system.

Watch this Scientific Journal Video about Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping at JoVE.com

Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

We present a method for collecting electrocorticographic signals for research purposes from humans who are undergoing invasive epilepsy monitoring. We show how to use the BCI2000 software platform for data collection, signal processing and stimulus presentation. Specifically, we demonstrate SIGFRIED, a BCI2000-based tool for real-time functional brain mapping.

Recording Human Electrocorticographic (ECoG) Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

Neuroimaging studies of human cognitive, sensory, and motor processes are usually based on noninvasive techniques such as electroencephalography (EEG), ...

recording-human-electrocorticographic-ecog-signals-for

Research

JoVE Journal

Neuroscience

25.5K Views.  New York State Department of Health. We present a method for collecting electrocorticographic signals for research purposes from humans who are undergoing invasive epilepsy monitoring. We show how to use the BCI2000 software platform for data collection, signal processing and stimulus presentation. Specifically, we demonstrate SIGFRIED, a BCI2000-based tool for real-time functional brain mapping.

Video: Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

Functional Mapping with Simultaneous MEG and EEG

We use magnetoencephalography (MEG) and electroencephalography (EEG) to locate and determine the temporal evolution in brain areas involved in the processing of simple sensory stimuli. We will use somatosensory stimuli to locate the hand somatosensory areas, auditory stimuli to locate the auditory cortices, visual stimuli in four quadrants of the visual field to locate the early visual areas. These type of experiments are used for functional mapping in epileptic and brain tumor patients to locate eloquent cortices. In basic neuroscience similar experimental protocols are used to study the orchestration of cortical activity. The acquisition protocol includes quality assurance procedures, subject preparation for the combined MEG/EEG study, and acquisition of evoked-response data with somatosensory, auditory, and visual stimuli. We also demonstrate analysis of the data using the equivalent current dipole model and cortically-constrained minimum-norm estimates. Anatomical MRI data are employed in the analysis for visualization and for deriving boundaries of tissue boundaries for forward modeling and cortical location and orientation constraints for the minimum-norm estimates.

We use magnetoencephalography (MEG) and electroencephalography (EEG) to map brain areas involved in the processing of simple sensory stimuli.

We use magnetoencephalography (MEG) and electroencephalography (EEG) to locate and determine the temporal evolution in brain areas involved in the ...

Correlating Behavioral Responses to fMRI Signals from Human Prefrontal Cortex: Examining Cognitive Processes Using Task Analysis

The aim of this methods paper is to describe how to implement a neuroimaging technique to examine complementary brain processes engaged by two similar tasks. Participants' behavior during task performance in an fMRI scanner can then be correlated to the brain activity using the blood-oxygen-level-dependent signal. We measure behavior to be able to sort correct trials, where the subject performed the task correctly and then be able to examine the brain signals related to correct performance. Conversely, if subjects do not perform the task correctly, and these trials are included in the same analysis with the correct trials we would introduce trials that were not only for correct performance. Thus, in many cases these errors can be used themselves to then correlate brain activity to them. We describe two complementary tasks that are used in our lab to examine the brain during suppression of an automatic responses: the stroop1 and anti-saccade tasks. The emotional stroop paradigm instructs participants to either report the superimposed emotional 'word' across the affective faces or the facial 'expressions' of the face stimuli1,2. When the word and the facial expression refer to different emotions, a conflict between what must be said and what is automatically read occurs. The participant has to resolve the conflict between two simultaneously competing processes of word reading and facial expression. Our urge to read out a word leads to strong 'stimulus-response (SR)' associations; hence inhibiting these strong SR's is difficult and participants are prone to making errors. Overcoming this conflict and directing attention away from the face or the word requires the subject to inhibit bottom up processes which typically directs attention to the more salient stimulus. Similarly, in the anti-saccade task3,4,5,6, where an instruction cue is used to direct only attention to a peripheral stimulus location but then the eye movement is made to the mirror opposite position. Yet again we measure behavior by recording the eye movements of participants which allows for the sorting of the behavioral responses into correct and error trials7 which then can be correlated to brain activity. Neuroimaging now allows researchers to measure different behaviors of correct and error trials that are indicative of different cognitive processes and pinpoint the different neural networks involved.

The goal of our research is to correlate behavior to brain activity. Accurate behavioral measures and imaging techniques allow us to elucidate brain-behavior relationships.

The aim of this methods paper is to describe how to implement a neuroimaging technique to examine complementary brain processes engaged by two similar ...

Functional Calcium Imaging in Developing Cortical Networks

A hallmark pattern of activity in developing nervous systems is spontaneous, synchronized network activity. Synchronized activity has been observed in intact spinal cord, brainstem, retina, cortex and dissociated neuronal culture preparations. During periods of spontaneous activity, neurons depolarize to fire single or bursts of action potentials, activating many ion channels. Depolarization activates voltage-gated calcium channels on dendrites and spines that mediate calcium influx. Highly synchronized electrical activity has been measured from local neuronal networks using field electrodes. This technique enables high temporal sampling rates but lower spatial resolution due to integrated read-out of multiple neurons at one electrode. Single cell resolution of neuronal activity is possible using patch-clamp electrophysiology on single neurons to measure firing activity. However, the ability to measure from a network is limited to the number of neurons patched simultaneously, and typically is only one or two neurons. The use of calcium-dependent fluorescent indicator dyes has enabled the measurement of synchronized activity across a network of cells. This technique gives both high spatial resolution and sufficient temporal sampling to record spontaneous activity of the developing network.
A key feature of newly-forming cortical and hippocampal networks during pre- and early postnatal development is spontaneous, synchronized neuronal activity (Katz &amp; Shatz, 1996; Khaziphov &amp; Luhmann, 2006). This correlated network activity is believed to be essential for the generation of functional circuits in the developing nervous system (Spitzer, 2006). In both primate and rodent brain, early electrical and calcium network waves are observed pre- and postnatally in vivo and in vitro (Adelsberger et al., 2005; Garaschuk et al., 2000; Lamblin et al., 1999). These early activity patterns, which are known to control several developmental processes including neuronal differentiation, synaptogenesis and plasticity (Rakic &amp; Komuro, 1995; Spitzer et al., 2004) are of critical importance for the correct development and maturation of the cortical circuitry.
In this JoVE video, we demonstrate the methods used to image spontaneous activity in developing cortical networks. Calcium-sensitive indicators, such as Fura 2-AM ester diffuse across the cell membrane where intracellular esterase activity cleaves the AM esters to leave the cell-impermeant form of indicator dye. The impermeant form of indicator has carboxylic acid groups which are able to then detect and bind calcium ions intracellularly.. The fluorescence of the calcium-sensitive dye is transiently altered upon binding to calcium. Single or multi-photon imaging techniques are used to measure the change in photons being emitted from the dye, and thus indicate an alteration in intracellular calcium. Furthermore, these calcium-dependent indicators can be combined with other fluorescent markers to investigate cell types within the active network.

Spontaneous activity of developing neuronal networks can be measured using AM-ester forms of calcium-sensitive indicator dyes. Changes in intracellular calcium, indicating neuronal activation, are detected as transient changes in indicator fluorescence with one- or two-photon imaging. This protocol can be adapted for a range of developmentally-dependent neuronal networks in vitro.

A hallmark pattern of activity in developing nervous systems is spontaneous, synchronized network activity. Synchronized activity has been observed in ...

Surgical Implantation of Chronic Neural Electrodes for Recording Single Unit Activity and Electrocorticographic Signals

The success of long-term electrophysiological recordings often depends on the quality of the implantation surgery. Here we provide useful information for surgeons who are learning the process of implanting electrode systems. We demonstrate the implantation procedure of both a penetrating and a surface electrode. The surgical process is described from start to finish, including detailed descriptions of each step throughout the procedure. It should also be noted that this video guide is focused towards procedures conducted in rodent models and other small animal models. Modifications of the described procedures are feasible for other animal models.

We provide useful information for surgeons who are learning the process of implanting chronic neural recording electrodes. Techniques for both penetrating and surface electrode systems are described in a rodent animal model.

The success of long-term electrophysiological recordings often depends on the quality of the implantation surgery.  Here we provide useful information for ...

Mapping Cortical Dynamics Using Simultaneous MEG/EEG and Anatomically-constrained Minimum-norm Estimates: an Auditory Attention Example

Magneto- and electroencephalography (MEG/EEG) are neuroimaging techniques that provide a high temporal resolution particularly suitable to investigate the cortical networks involved in dynamical perceptual and cognitive tasks, such as attending to different sounds in a cocktail party. Many past studies have employed data recorded at the sensor level only, i.e., the magnetic fields or the electric potentials recorded outside and on the scalp, and have usually focused on activity that is time-locked to the stimulus presentation. This type of event-related field / potential analysis is particularly useful when there are only a small number of distinct dipolar patterns that can be isolated and identified in space and time. Alternatively, by utilizing anatomical information, these distinct field patterns can be localized as current sources on the cortex. However, for a more sustained response that may not be time-locked to a specific stimulus (e.g., in preparation for listening to one of the two simultaneously presented spoken digits based on the cued auditory feature) or may be distributed across multiple spatial locations unknown a priori, the recruitment of a distributed cortical network may not be adequately captured by using a limited number of focal sources.
Here, we describe a procedure that employs individual anatomical MRI data to establish a relationship between the sensor information and the dipole activation on the cortex through the use of minimum-norm estimates (MNE). This inverse imaging approach provides us a tool for distributed source analysis. For illustrative purposes, we will describe all procedures using FreeSurfer and MNE software, both freely available. We will summarize the MRI sequences and analysis steps required to produce a forward model that enables us to relate the expected field pattern caused by the dipoles distributed on the cortex onto the M/EEG sensors. Next, we will step through the necessary processes that facilitate us in denoising the sensor data from environmental and physiological contaminants. We will then outline the procedure for combining and mapping MEG/EEG sensor data onto the cortical space, thereby producing a family of time-series of cortical dipole activation on the brain surface (or "brain movies") related to each experimental condition. Finally, we will highlight a few statistical techniques that enable us to make scientific inference across a subject population (i.e., perform group-level analysis) based on a common cortical coordinate space.

We use magneto- and electroencephalography (MEG/EEG), combined with anatomical information captured by magnetic resonance imaging (MRI), to map the dynamics of the cortical network associated with auditory attention.

Magneto- and electroencephalography (MEG/EEG) are neuroimaging techniques that provide a high temporal resolution particularly suitable to investigate the ...

Functional Imaging of Auditory Cortex in Adult Cats using High-field fMRI

Current knowledge of sensory processing in the mammalian auditory system is mainly derived from electrophysiological studies in a variety of animal models, including monkeys, ferrets, bats, rodents, and cats. In order to draw suitable parallels between human and animal models of auditory function, it is important to establish a bridge between human functional imaging studies and animal electrophysiological studies. Functional magnetic resonance imaging (fMRI) is an established, minimally invasive method of measuring broad patterns of hemodynamic activity across different regions of the cerebral cortex. This technique is widely used to probe sensory function in the human brain, is a useful tool in linking studies of auditory processing in both humans and animals and has been successfully used to investigate auditory function in monkeys and rodents. The following protocol describes an experimental procedure for investigating auditory function in anesthetized adult cats by measuring stimulus-evoked hemodynamic changes in auditory cortex using fMRI. This method facilitates comparison of the hemodynamic responses across different models of auditory function thus leading to a better understanding of species-independent features of the mammalian auditory cortex.

Functional studies of the auditory system in mammals have traditionally been conducted using spatially-focused techniques such as electrophysiological recordings. The following protocol describes a method of visualizing large-scale patterns of evoked hemodynamic activity in the cat auditory cortex using functional magnetic resonance imaging.

Current knowledge of sensory processing in the mammalian auditory system is mainly derived from electrophysiological studies in a variety of animal ...

A Protocol for the Administration of Real-Time fMRI Neurofeedback Training

Neurologic disorders are characterized by abnormal cellular-, molecular-, and circuit-level functions in the brain. New methods to induce and control neuroplastic processes and correct abnormal function, or even shift functions from damaged tissue to physiologically healthy brain regions, hold the potential to dramatically improve overall health. Of the current neuroplastic interventions in development, neurofeedback training (NFT) from functional Magnetic Resonance Imaging (fMRI) has the advantages of being completely non-invasive, non-pharmacologic, and spatially localized to target brain regions, as well as having no known side effects. Furthermore, NFT techniques, initially developed using fMRI, can often be translated to exercises that can be performed outside of the scanner without the aid of medical professionals or sophisticated medical equipment. In fMRI NFT, the fMRI signal is measured from specific regions of the brain, processed, and presented to the participant in real-time. Through training, self-directed mental processing techniques, that regulate this signal and its underlying neurophysiologic correlates, are developed. FMRI NFT has been used to train volitional control over a wide range of brain regions with implications for several different cognitive, behavioral, and motor systems. Additionally, fMRI NFT has shown promise in a broad range of applications such as the treatment of neurologic disorders and the augmentation of baseline human performance. In this article, we present an fMRI NFT protocol developed at our institution for modulation of both healthy and abnormal brain function, as well as examples of using the method to target both cognitive and auditory regions of the brain.

The ability to induce and/or control neural plasticity may be critical in future treatments for neurologic disorders and the recovery from brain injury. In this paper, we present a protocol on the use of neurofeedback training with functional magnetic resonance imaging to modulate human brain function.

Neurologic disorders are characterized by abnormal cellular-, molecular-, and circuit-level functions in the brain. New methods to induce and control ...

Chronic Implantation of Whole-cortical Electrocorticographic Array in the Common Marmoset

Electrocorticography (ECoG) allows the monitoring of electrical field potentials from the cerebral cortex with high spatiotemporal resolution. Recent development of thin, flexible ECoG electrodes has enabled conduction of stable recordings of large-scale cortical activity. We have developed a whole-cortical ECoG array for the common marmoset. The array continuously covers almost the entire lateral surface of cortical hemisphere, from the occipital pole to the temporal and frontal poles, and it captures whole-cortical neural activity in one shot. This protocol describes a chronic implantation procedure of the array in the epidural space of the marmoset brain. Marmosets have two advantages regarding ECoG recordings, one being the homologous organization of anatomical structures in humans and macaques, including frontal, parietal, and temporal complexes. The other advantage is that the marmoset brain is lissencephalic and contains a large number of complexes, which are more difficult to access in macaques with ECoG, that are exposed to the brain surface.These features allow direct access to most cortical areas beneath the surface of the brain. This system provides an opportunity to investigate global cortical information processing with high resolutions at a sub-millisecond order in time and millimeter order in space.

We have developed a whole-cortical electrocorticographic array for the common marmoset that continuously covers almost the entire lateral surface of cortex, from the occipital pole to the temporal and frontal poles. This protocol describes a chronic implantation procedure of the array in the epidural space of the marmoset brain.

Electrocorticography (ECoG) allows the monitoring of electrical field potentials from the cerebral cortex with high spatiotemporal resolution. Recent ...

Real-Time fMRI Brain Mapping in Animals

Dynamic fMRI responses vary largely according to the physiological conditions of animals either under anesthesia or in awake states. We developed a real-time fMRI platform to guide experimenters to monitor fMRI responses instantaneously during acquisition, which can be used to modify the physiology of animals to achieve desired hemodynamic responses in animal brains. The real-time fMRI set-up is based on a 14.1T preclinical MRI system, enabling the real-time mapping of dynamic fMRI responses in the primary forepaw somatosensory cortex (FP-S1) of anesthetized rats. Instead of a retrospective analysis to investigate confounding sources leading to the variability of fMRI signals, the real-time fMRI platform provides a more effective scheme to identify dynamic fMRI responses using customized macro-functions and a common neuroimage analysis software in the MRI system. Also, it provides immediate troubleshooting feasibility and a real-time biofeedback stimulation paradigm for brain functional studies in animals.

Animal brain functional mapping can benefit from the real-time functional magnetic resonance imaging (fMRI) experimental set-up. Using the latest software implemented in the animal MRI system, we established a real-time monitoring platform for small animal fMRI.

Dynamic fMRI responses vary largely according to the physiological conditions of animals either under anesthesia or in awake states. We developed a ...

Electrocorticographic Recording of Cerebral Cortex Areas Manipulated Using an Adeno-Associated Virus Targeting Cofilin in Mice

The use of electrocorticographic (ECoG) recordings in rodents is relevant to sleep research and to the study of a wide range of neurological conditions. Adeno-associated viruses (AAVs) are increasingly used to improve understanding of brain circuits and their functions. The AAV-mediated manipulation of specific cell populations and/or of precise molecular components has been tremendously useful to identify new sleep regulatory circuits/molecules and key proteins contributing to the adverse effects of sleep loss. For instance, inhibiting activity of the filamentous actin-severing protein&#160;cofilin&#160;using AAV prevents sleep deprivation-induced memory impairment. Here, a protocol is&#160;described that combines the manipulation of cofilin function in a cerebral cortex area with the recording of ECoG activity to examine whether cortical cofilin modulates the wakefulness and sleep ECoG signals. AAV injection is performed during the same surgical procedure as the implantation of ECoG and electromyographic (EMG) electrodes in adult male and female mice. Mice are anesthetized, and their heads are shaved. After skin cleaning and incision, stereotaxic coordinates of the motor cortex are determined, and the skull is pierced at this location. A cannula prefilled with an AAV expressing cofilinS3D, an inactive form of cofilin, is slowly positioned in the cortical tissue. After AAV infusion, gold-covered screws (ECoG electrodes) are screwed through the skull and cemented to the skull with gold wires inserted in the neck muscles (EMG electrodes). The animals are allowed three weeks to recover and to ensure sufficient expression of cofilinS3D. The infected area and cell type are verified using immunohistochemistry, and the ECoG is analyzed using visual identification of vigilance states and spectral analysis. In summary, this combined methodological approach allows the investigation of the precise contribution of molecular components regulating neuronal morphology and connectivity to the regulation of synchronized cerebral cortex activity during wakefulness and sleep.

This article describes a protocol for the manipulation of molecular targets in the cerebral cortex using adeno-associated viruses and for monitoring the effects of this manipulation during wakefulness and sleep using electrocorticographic recordings.

The use of electrocorticographic (ECoG) recordings in rodents is relevant to sleep research and to the study of a wide range of neurological conditions. ...