This research was supported by the following funding sources: A NARSAD Young Investigator Award Grant from the Brain and Behavior Research Foundation (Grant #29736) (SSA), a Global Grand Challenges Grant from the Bill and Melinda Gates Foundation (Grant #INV-005792) (RNA) and a Discovery Fund Grant from the Department of Psychology at Yale University (RNA). The authors also wish to acknowledge Richard Watts (Yale Brain Imaging Center) for his support during data collection and Adam Eggebrecht, Ari Segel and Emma Speh (Washington University in St Louis) for their assistance in data analysis.

Publication fees for this article are sponsored by NIRx. The authors have nothing else to disclose.

This protocol for simultaneous data collection of fMRI&#160;and fNIRS signals uses a whole-head fNIRS optode array and short-distance channels for measuring and regressing out the systemic non-cortical physiological signals. Critical steps in this protocol include modification and development of the fNIRS equipment for collecting fNIRS signals in the MRI environment. To the best of our knowledge, there is no turn-key commercial system that is fully optimized for capturing simultaneous fMRI&#160;and fNIRS measurements using a whole-head fNIRS array. The present protocol addresses this gap and will be particularly relevant for those researchers interested in a whole-head comparison of the two signals, although it can easily be modified for studies investigating specific regions of interest.
The protocol outlines in detail key modifications to the fNIRS equipment, including fNIRS cap preparation with inserts to store vitamin E capsules, cap improvements to increase comfort in frontal areas and adjustability at the back of the head, and a custom-made MR safe bridge to bring the fNIRS optical fibers onto the scanner table. One of the key challenges when conducting a simultaneous fMRI/fNIRS study is to ensure that the setup allows participants to rest comfortably in the scanner. The current setup with adults allows scanning sessions for an average of approximately 40 min, which includes both functional and structural scans. The amount of time participants can rest comfortably in the scanner will be primarily determined by the type of optodes provided with the fNIRS system. The present protocol uses a NIRx NIRScout XP system that has low-profile optodes with a flat surface, which allows most adult subjects to rest comfortably in the scanner for the entire duration of the study. Finally, the protocol also includes steps for temporal alignment of the two data streams via trigger synchronization across modalities, fNIRS cap placement, participant setup and signal recording.
Limitations and potential challenges 
The protocol may need to be modified to fit the specifics of the available fNIRS instrument. A crucial first step is to check with the fNIRS vendor to ensure that the optodes and optical fibers are suitable for data collection in the MR environment. fNIRS systems are likely to vary with respect to the type of caps and optodes. Well-fitted caps and low-profile optodes with a flat surface are recommended. Alternatively, prior work has described the use of custom-made support systems to avoid applying pressure on the fNIRS optodes32.
Another aspect that is likely to vary across fNIRS devices is the triggering system available for signal synchronization across modalities. The present protocol uses a parallel port replicator box to receive the TTL pulses from the scanner and send triggers to the fNIRS acquisition software. Given that this is a key step to ensure synchronization across modalities, the researcher should consult with their fNIRS vendor on the recommended system for signal synchronization.
Finally, the current protocol uses 8 short-distance channels, which are currently only available for a limited number of fNIRS systems. If short-distance channels are not available, an alternative is to implement some of the recent analytic approaches for identification and removal of the systemic physiological signal18,25,48,49,50,51. For a recent quantitative comparison of available correction techniques see52.
Applications of the protocol for testing developmental and clinical populations 
The protocol can be modified for data collection of fMRI&#160;and fNIRS signals with developmental and clinical populations. Potential adjustments necessary for these populations include cap sizes (since the caps are age- and head-size specific), the addition of a training session to familiarize the participant with the scanner environment, and the inclusion of shorter scanning sessions&#160;&#8211;&#160;all of which are particularly relevant when testing infants and young children. Furthermore, the benefits of using short-distance channels in infants and young children are still unclear53, although prior studies have shown that 10 mm distance channels do seem to capture extracerebral hemodynamics in infants53,54. Monte Carlo simulations of photon transport indicate that different optimum source-detector distances are needed for short-separation channels in adults and newborns as a function of age and optode location on the scalp55. However, further research is needed to create standardized approaches to perform short separation regression in infants and young children. Finally, studies that rely on good quality auditory stimuli will need to carefully consider the available systems for delivery of audio in the MRI scanner. Active noise-cancelling headphones currently used with adults may get easily displaced due to head motion when used with awake infants and toddlers. In such cases, infant-specific headphones should be used. Alternatively, infants can participate in a training session prior to the scan in order to minimize head motion, although this option may only work for older infants.
Conclusion 
The protocol allows simultaneous data collection of fMRI&#160;and fNIRS signals. In contrast to available methods, it implements a whole-head fNIRS array and includes short-distance channel measurements. Furthermore, two different methods for optode-to-scalp co-registration of the fNIRS signals are described: i) vitamin E capsules attached to each optode on the fNIRS caps and ii) a 3D structure sensor that allows digitization of the optode locations with respect to fiducial markers on the head. The current protocol can be easily adapted to collect data from specific regions of interest and across a variety of experimental paradigms. Although the current protocol has been tested with young adults, suggestions on how to adapt it for use with developmental and clinical populations are also provided. This protocol will be particularly relevant for those interested in validating fNIRS area-level activations and functional connectivity against fMRI across the lifespan.

Cognitive function has been studied in the adult human brain via functional magnetic resonance imaging (fMRI) for nearly three decades. Although fMRI provides high spatial resolution and both functional and structural images, it is often not practical for studies conducted in naturalistic contexts or for use with infants and clinical populations. These constraints substantially limit our understanding of brain function. An alternative to fMRI is the use of portable methodologies that are more cost-effective and robust to motion, such as functional near-infrared spectroscopy (fNIRS)1,2,3. fNIRS has been used with infants and young children to assess brain function across a range of cognitive domains, such as language development, processing of socially relevant information and object processing 4,5,6. fNIRS is also a neuroimaging modality especially suitable for testing clinical populations due to its potential for repeated testing and monitoring across ages7,8,9. Despite its wide applicability, there are no studies quantitatively comparing fMRI and fNIRS signals collected simultaneously from the same subjects with whole-head coverage. This comparison is necessary to comprehensively validate area-level activations and functional connectivity between regions of interest (ROIs) against the fMRI gold standard. Furthermore, establishing this inter-modality correspondence has the potential to enhance the interpretation of fNIRS when it is the only collected signal across both typical and atypical development.
Both fMRI and fNIRS signals detect changes in cerebral blood oxygenation (CBO) during functional brain activation10,11. fMRI relies on changes in electromagnetic fields and provides a high spatial resolution of CBO changes12. fNIRS, in contrast, measures absorption levels of near-infrared light using a series of light-emitting and light-detecting optodes2. Since fNIRS measures changes in absorption at different wavelengths, it can assess concentration changes in both oxy- and deoxyhemoglobin. Prior studies using simultaneous recordings of fMRI and fNIRS signals with a small number of optodes have shown that the two signals have high spatial and temporal correspondence10. There are strong correlations between blood-oxygen-level-dependent (BOLD) fMRI and optical measures11,13, with deoxyhemoglobin showing the highest correlation with the BOLD response, as reported by prior work comparing the temporal dynamics of the fNIRS and fMRI hemodynamic response functions (HRFs)14. These early studies implemented motor response paradigms (i.e., finger tapping) and used a limited number of optodes covering primary motor and premotor cortex areas. In the last decade, studies have expanded the focus to include a larger battery of cognitive tasks and resting-state sessions, although still using a limited number of optodes covering specific ROIs. These studies have shown that variability in fNIRS/fMRI correlations is dependent on the optode&#39;s distance from the scalp and the brain15. Furthermore, fNIRS can provide resting-state functional connectivity measures comparable to fMRI16,17.
The current protocol builds on prior work and addresses key limitations by i) providing whole-head fNIRS coverage, ii) including short-distance measurements for regression of non-cortical physiological signals, iii) implementing two different methods for optode-to-scalp co-registration of fNIRS measurements and iv) enabling assessment of the test-retest reliability of the signal across two independent sessions. This protocol for simultaneous data collection of fMRI&#160;and fNIRS signals was initially developed for testing young adults. However, one of the goals of the study was to create an experimental setup for collecting simultaneous fMRI/fNIRS signals that can be subsequently adapted for testing developmental populations. Therefore, the current protocol can also be used as a starting point for developing a protocol to test young children. In addition to using whole-head fNIRS coverage, the protocol also aims to incorporate recent advances in the field of fNIRS hardware, such as the inclusion of short-distance channels to measure the systemic physiological signal (i.e., vascular changes arising from noncortical sources, such as blood pressure, respiratory and cardiac signals)18,19 ;and the use of a 3D structure sensor for optode-to-scalp co-registration20. Although the focus of the present protocol is on the results of a visual flashing checkerboard task, the entire experiment includes two sessions with a mix of traditional block-task designs, resting-state sessions, and naturalistic movie-viewing paradigms.
The protocol describes the steps needed to adapt the fNIRS equipment for use in the MRI environment, including cap design, temporal alignment via trigger synchronization and phantom tests required before the start of data collection. As noted, the focus here is on the results of the flashing checkerboard task, but the overall procedure is not task-specific and can be appropriate for any number of experimental paradigms. The protocol further outlines the steps required during data collection, which include fNIRS cap placement and signal calibration, participant&#160;and experimental equipment setup, as well as post-experiment clean up and data storage. The protocol ends by providing an overview of the analytic pipelines specific for preprocessing fNIRS and fMRI data.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>280 low-profile MRI-compatible grommets for NIRs caps</td>
			<td>NIRx</td>
			<td>GRM-LOP</td>
			<td></td>
		</tr>
		<tr>
			<td>4 128-position NIRS caps with 128x unpopulated slits in 10-5 layout</td>
			<td>NIRx</td>
			<td>CP-128-128S</td>
			<td>Sizes: 52, 54, 56, 60</td>
		</tr>
		<tr>
			<td>8 bundles of 4x detector fibers with low-profile tip; MRI-, MEG-, and TMS-compatible.&#160;</td>
			<td>NIRx</td>
			<td>DET-FBO- LOW</td>
			<td>10 m long</td>
		</tr>
		<tr>
			<td>8 bundles of 4x laser source fibers with MRI-compatible low-profile tip</td>
			<td>NIRx</td>
			<td>SRC-FBO- LAS-LOW</td>
			<td>10 m long</td>
		</tr>
		<tr>
			<td>Bundle set of 8 short-channel detectors with specialized ring grommets that fit to low-profile grommets</td>
			<td>NIRx</td>
			<td>DET-SHRT-SET</td>
			<td>Splits a single detector into 8 short channels that may be placed anywhere on a single NIRS cap</td>
		</tr>
		<tr>
			<td>Magnetom 3T PRISMA</td>
			<td>Siemens</td>
			<td>N/A</td>
			<td>128 channel capacity, 64/32/20 channel head coils, 80 mT/m max gradient amplitude, 200 T/m/s slew rate, full neuro sequences</td>
		</tr>
		<tr>
			<td>NIRScout XP Core System Unit</td>
			<td>NIRx</td>
			<td>NSXP- CHS</td>
			<td>Up to 64x Laser-2 (or 32x laser-4) illuminators or 64 LED-2 illuminators; up to 32x detectors; capable of tandem (multi-system) and hyperscanning (multi-subject) measurements; compatible with EEG, tDCS, eye-tracking, and other modalities; modules available for fMRI, TMS, MEG compatibility</td>
		</tr>
		<tr>
			<td>NIRStar software</td>
			<td>NIRx</td>
			<td>N/A</td>
			<td>Version 15.3</td>
		</tr>
		<tr>
			<td>NIRx parallel port replicator</td>
			<td>NIRx</td>
			<td>ACC-LPT-REP</td>
			<td>The parallel prot replicator&#160; comes with three components: parallel port replicator box, USB power cable and BNC adapter</td>
		</tr>
		<tr>
			<td>Physiological pulse unit</td>
			<td>Siemens</td>
			<td>PPU098</td>
			<td>Optical plethysmography allowing the acquisiton of the cardiac rhythm.</td>
		</tr>
		<tr>
			<td>Respiratory unit</td>
			<td>Siemens</td>
			<td>PERU098&#160;</td>
			<td>Unit intended for the acquisition of the respiratory amplitude (by means of a pneumatic system and a restraint belt).</td>
		</tr>
		<tr>
			<td>Structure Sensor Mark II</td>
			<td>Occipital</td>
			<td>101866 (SN)</td>
			<td>3D structure sensor for optode digitization.</td>
		</tr>
	</tbody>
</table>

simultaneous data collection of fmri and fnirs measurements using a whole-head optode array and short-distance channels

Functional near-infrared spectroscopy (fNIRS) is a portable neuroimaging methodology, more robust to motion and more cost-effective than functional magnetic resonance imaging (fMRI), which makes it highly suitable for conducting naturalistic studies of brain function and for use with developmental and clinical populations. Both fNIRS and fMRI methodologies detect changes in cerebral blood oxygenation during functional brain activation, and prior studies have shown high spatial and temporal correspondence between the two signals. There is, however, no quantitative comparison of the two signals collected simultaneously from the same subjects with whole-head fNIRS coverage. This comparison is necessary to comprehensively validate area-level activations and functional connectivity against the fMRI gold standard, which in turn has the potential to facilitate comparisons of the two signals across the lifespan. We address this gap by describing a protocol for simultaneous data collection of fMRI&#160;and fNIRS signals that: i) provides whole-head fNIRS coverage; ii) includes short-distance measurements for regression of the non-cortical, systemic physiological signal; and iii) implements two different methods for optode-to-scalp co-registration of fNIRS measurements. fMRI and fNIRS data from three subjects are presented, and recommendations for adapting the protocol to test developmental and clinical populations are discussed. The current setup with adults allows scanning sessions for an average of approximately 40 min, which includes both functional and structural scans. The protocol outlines the steps required to adapt the fNIRS equipment for use in the magnetic resonance (MR) environment, provides recommendations for both data recording and optode-to-scalp co-registration, and discusses potential modifications of the protocol to fit the specifics of the available MR-safe fNIRS system. Representative subject-specific responses from a flashing-checkerboard task illustrate the feasibility of the protocol to measure whole-head fNIRS signals in the MR environment. This protocol will be particularly relevant for researchers interested in validating fNIRS signals against fMRI across the lifespan.

This section presents representative subject-specific responses for the flashing checkerboard task for both fMRI and fNIRS signals. First, representative raw fNIRS data and quality assessments are shown in Figure 6 and Figure 7 to illustrate the feasibility of the experimental setup to measure fNIRS signals in the MRI environment. A diagram of the whole head optode array and sensitivity profile is shown in Figure 8. 
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/65088/65088fig06.jpg" /> 
Figure 6. Representative fNIRS time-series data after bandpass filtering and superficial signal regression. Left column shows data at 785 nm and right column shows data at 830 nm. (A) fNIRS data timeseries after applying band pass filter (high pass filter cutoff: 0.02 Hz, low pass filter cutoff: 0.5 Hz cutoff) and global signal regression. The y-axis is log scaled to highlight the range of light levels for the set of source-detector distances. Vertical lines indicate time points where a new block begins in the stimulus paradigm. Green lines indicate the start of the flashing checkerboard block and blue lines indicate the start of the inter-trial period. (B) Spectrum of the fNIRS signal after applying the band pass filter (high pass filter cutoff: 0.02 Hz, low pass filter cutoff: 0.5 Hz cutoff) and global signal regression. Frequencies below the cutoff frequency are significantly attenuated. The spectrum shows a much stronger peak at the stimulus frequency, that is at the onset of the flashing checkerboard blocks (0.033 Hz), relative to other frequencies. <a href="https://www.jove.com/files/ftp_upload/65088/65088fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/65088/65088fig07.jpg" /> 
Figure 7. fNIRS data quality assessment for a single subject. (A) Average light levels for a single subject across the entire fNIRS data stream. White and yellow colors serve as qualitative assessments of optimal coupling for each optode. (B) Signal-to-noise ratio (SNR) across measurements for a single subject across the entire fNIRS data stream. White and yellow colors indicate good SNR. Optodes located on the upper part of the fNIRS cap over sensorimotor regions tend to have lower SNR (typically due to dense hair or a loose-fitting cap). (C) The temporal variance in all 100 source-detector pairs is used to evaluate and optimize data quality. Pairs with variance below 7.5% (red line) are retained for further analysis. (D) Measurements that satisfy the noise threshold (i.e., variance above 7.5%). For this participant, 97% of the optodes are considered acceptable. <a href="https://www.jove.com/files/ftp_upload/65088/65088fig07large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 8" class="xfigimg" src="/files/ftp_upload/65088/65088fig08.jpg" /> 
Figure 8. Whole-head optode array setup and sensitivity profile. (A) Optode array setup with 32/30 sources/detectors resulting in 100 channels with whole head coverage and 30-mm separation and 8 short-distance channels with 8-mm separation. (B) Sensitivity profile for the optode array given the specified parameters for Tikhonov regularization (0.01, 0.1). Unit represents percentage of the flat field. Areas with high confidence typically have a flat field value higher than ~0.5%-1% <a href="https://www.jove.com/files/ftp_upload/65088/65088fig08large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
After data pre-processing, fNIRS and fMRI responses for the flashing-checkerboard task were estimated using a standard general linear model (GLM) framework. The design matrix was constructed using onsets and durations of each stimulus presentation convolved with a canonical HRF. For fNIRS the delta HbO results are shown given that the oxy-haemoglobin (&#916;HbO) signal exhibits a higher contrast-to-noise ratio compared to deoxy-haemoglobin (&#916;HbR) or total haemoglobin (&#916;HbT)44,47. Subject-level fNIRS data show increased activation in bilateral visual cortex areas during the flashing checkerboard blocks compared to the inter-trial periods. Time traces of brain activity in visual cortex show an increase of HbO signal during the presentation of the flashing checkerboard and a decrease during inter-trial periods (Figure 9A). This hemodynamic increase in response to flashing checkerboard periods is not observed in an unrelated brain area (Figure 9B). As expected, visualization of the HbO data during the flashing checkerboard period shows bilateral activation in visual cortex areas (Figure 9C).
<img alt="Figure 9" class="xfigimg" src="/files/ftp_upload/65088/65088fig09.jpg" /> 
Figure 9. Time traces of fNIRS HbO responses during the experimental paradigm. Time traces are shown for (A) activity in visual cortex during a flashing checkerboard block, (B) activity in visual cortex area between flashing checkerboard blocks, and (C) activity in an unrelated brain area during a flashing checkerboard block. <a href="https://www.jove.com/files/ftp_upload/65088/65088fig09large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 10" class="xfigimg" src="/files/ftp_upload/65088/65088fig10.jpg" /> 
Figure 10. Representative single-subject fNIRS HbO responses during the flashing checkerboard period. Maps of block averaged (HbO) data from the start of the flashing checkerboard shown for three subjects. Data includes the 10 s flashing checkerboard period and 5 s after to assess brain activation in response to the stimulus. <a href="https://www.jove.com/files/ftp_upload/65088/65088fig10large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Subject-level fMRI data show greater BOLD signal response in primary and secondary visual cortex during the flashing checkerboard periods relative to the inter-trial periods (Figure 11A). At the subcortical level, increased activation is observed in the lateral geniculate nucleus (LGN) of the thalamus, which is expected since the LGN receives visual input from the retina (Figure 11B).
<img alt="Figure 11" class="xfigimg" src="/files/ftp_upload/65088/65088fig11.jpg" /> 
Figure 11. Representative single-subject fMRI activation estimates during the flashing checkerboard period. (Top Row) Activation (beta) estimates for three subjects obtained from first level statistical analysis and showing bilateral engagement of primary and secondary visual cortex areas during the flashing checkerboard period. (Bottom Row) Subcortical activation estimates showing engagement of the lateral geniculate nucleus (LGN) during the flashing checkerboard period, which serves as a qualitative assessment that the fMRI data are collected as expected with the 20-channel head coil. The red arrow points to the location of the LGN on the brain map. <a href="https://www.jove.com/files/ftp_upload/65088/65088fig11large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Altogether, these results illustrate the feasibility of implementing the current protocol to collect simultaneous fMRI and fNIRS signals with an adult population. The protocol allows for a total of 40 min of scanning time and affords full-head coverage of the fNIRS data. We have discussed data collection with a visual flashing-checkerboard paradigm, but the protocol is also applicable to other experimental paradigms. We recommend assessing the sensitivity profile of the fNIRS array in advance to ensure maximal sensitivity across relevant channels to the underlying cortical regions of interest.

Watch this Scientific Journal Video about Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels at JoVE.com

Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels

We present a method for simultaneously collecting fMRI and fNIRS signals from the same subjects with whole-head fNIRS coverage. The protocol has been tested with three young adults and can be adapted for data collection for developmental studies and clinical populations.

Functional near-infrared spectroscopy (fNIRS) is a portable neuroimaging methodology, more robust to motion and more cost-effective than functional ...

simultaneous-data-collection-fmri-fnirs-measurements-using-whole-head

Nanyang Technological University

Research

JoVE Journal

Neuroscience

930 Views.  Yale University School of Medicine. We present a method for simultaneously collecting fMRI and fNIRS signals from the same subjects with whole-head fNIRS coverage. The protocol has been tested with three young adults and can be adapted for data collection for developmental studies and clinical populations. 

Video: Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels

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 ...

Multielectrode Array Recordings of the Vomeronasal Epithelium

Understanding neural circuits requires methods to record from many neurons simultaneously. For in vitro studies, one currently available technology is planar multielectrode array (MEA) recording. Here we document the use of MEAs to study the mouse vomeronasal organ (VNO), which plays an essential role in the detection of pheromones and social cues via a diverse population of sensory neurons expressing hundreds of types of receptors. Combining MEA recording with a robotic liquid handler to deliver chemical stimuli, the sensory responses of a large and diverse population of neurons can be recorded. The preparation allows us to remove the intact neuroepithelium of the VNO from the mouse and stimulate with a battery of chemicals or potential ligands while monitoring the electrical activity of the neurons for several hours. Therefore, this technique serves as a useful method for assessing ligand activity as well as exploring the properties of receptor neurons. We present the techniques needed to prepare the vomeronasal epithelium, MEA recording, and chemical stimulation.

Multielectrode array (MEA) recordings provide a method for studying the electrical activity of large populations of neurons. Here, we present the details of a MEA preparation to record from the mouse vomeronasal epithelium while simultaneously stimulating the tissue.

Understanding neural circuits requires methods to record from many neurons simultaneously. For in vitro studies, one currently available technology is ...

Simultaneous fMRI and Electrophysiology in the Rodent Brain

To examine the neural basis of the blood oxygenation level dependent (BOLD) magnetic resonance imaging (MRI) signal, we have developed a rodent model in which functional MRI data and in vivo intracortical recording can be performed simultaneously. The combination of MRI and electrical recording is technically challenging because the electrodes used for recording distort the MRI images and the MRI acquisition induces noise in the electrical recording. To minimize the mutual interference of the two modalities, glass microelectrodes were used rather than metal and a noise removal algorithm was implemented for the electrophysiology data. In our studies, two microelectrodes were separately implanted in bilateral primary somatosensory cortices (SI) of the rat and fixed in place. One coronal slice covering the electrode tips was selected for functional MRI. Electrode shafts and fixation positions were not included in the image slice to avoid imaging artifacts. The removed scalp was replaced with toothpaste to reduce susceptibility mismatch and prevent Gibbs ringing artifacts in the images. The artifact structure induced in the electrical recordings by the rapidly-switching magnetic fields during image acquisition was characterized by averaging all cycles of scans for each run. The noise structure during imaging was then subtracted from original recordings. The denoised time courses were then used for further analysis in combination with the fMRI data. As an example, the simultaneous acquisition was used to determine the relationship between spontaneous fMRI BOLD signals and band-limited intracortical electrical activity. Simultaneous fMRI and electrophysiological recording in the rodent will provide a platform for many exciting applications in neuroscience in addition to elucidating the relationship between the fMRI BOLD signal and neuronal activity.

We have developed a method for simultaneous functional magnetic resonance imaging and electrophysiological recording in the rodent brain, providing a platform for the investigation of the relationship between neural activity and the blood oxygenation level dependent (BOLD) MRI signal.

To examine the neural basis of the blood oxygenation level dependent (BOLD) magnetic resonance imaging (MRI) signal, we have developed a rodent model in ...

Combining Transcranial Magnetic Stimulation and fMRI to Examine the Default Mode Network

The default mode network is a group of brain regions that are active when an individual is not focused on the outside world and the brain is at "wakeful rest."1,2,3 It is thought the default mode network corresponds to self-referential or "internal mentation".2,3
It has been hypothesized that, in humans, activity within the default mode network is correlated with certain pathologies (for instance, hyper-activation has been linked to schizophrenia 4,5,6 and autism spectrum disorders 7 whilst hypo-activation of the network has been linked to Alzheimer's and other neurodegenerative diseases 8). As such, noninvasive modulation of this network may represent a potential therapeutic intervention for a number of neurological and psychiatric pathologies linked to abnormal network activation. One possible tool to effect this modulation is Transcranial Magnetic Stimulation: a non-invasive neurostimulatory and neuromodulatory technique that can transiently or lastingly modulate cortical excitability (either increasing or decreasing it) via the application of localized magnetic field pulses.9
In order to explore the default mode network's propensity towards and tolerance of modulation, we will be combining TMS (to the left inferior parietal lobe) with functional magnetic resonance imaging (fMRI). Through this article, we will examine the protocol and considerations necessary to successfully combine these two neuroscientific tools.

In this article, we examine the methodology and considerations relevant to the combination of TMS and fMRI to examine the effects of brain stimulation on the default network.

The default mode network is a group of brain regions that are active when an individual is not focused on the outside world and the brain is at "wakeful ...

Electrophysiological Measurements and Analysis of Nociception in Human Infants

Pain is an unpleasant sensory and emotional experience. Since infants cannot verbally report their experiences, current methods of pain assessment are based on behavioural and physiological body reactions, such as crying, body movements or changes in facial expression. While these measures demonstrate that infants mount a response following noxious stimulation, they are limited: they are based on activation of subcortical somatic and autonomic motor pathways that may not be reliably linked to central sensory processing in the brain. Knowledge of how the central nervous system responds to noxious events could provide an insight to how nociceptive information and pain is processed in newborns.
The heel lancing procedure used to extract blood from hospitalised infants offers a unique opportunity to study pain in infancy. In this video we describe how electroencephalography (EEG) and electromyography (EMG) time-locked to this procedure can be used to investigate nociceptive activity in the brain and spinal cord.
This integrative approach to the measurement of infant pain has the potential to pave the way for an effective and sensitive clinical measurement tool.

The assessment and treatment of pain in infants is difficult because infants cannot verbally report their experience. In this video we describe quantitative electrophysiological methods and analysis techniques that can be used to measure the response to noxious events from the infant nervous system.

Pain is an unpleasant sensory and emotional experience. Since infants cannot verbally report their experiences, current methods of pain assessment are ...

Co-analysis of Brain Structure and Function using fMRI and Diffusion-weighted Imaging

The study of complex computational systems is facilitated by network maps, such as circuit diagrams. Such mapping is particularly informative when studying the brain, as the functional role that a brain area fulfills may be largely defined by its connections to other brain areas. In this report, we describe a novel, non-invasive approach for relating brain structure and function using magnetic resonance imaging (MRI). This approach, a combination of structural imaging of long-range fiber connections and functional imaging data, is illustrated in two distinct cognitive domains, visual attention and face perception. Structural imaging is performed with diffusion-weighted imaging (DWI) and fiber tractography, which track the diffusion of water molecules along white-matter fiber tracts in the brain (Figure 1). By visualizing these fiber tracts, we are able to investigate the long-range connective architecture of the brain. The results compare favorably with one of the most widely-used techniques in DWI, diffusion tensor imaging (DTI). DTI is unable to resolve complex configurations of fiber tracts, limiting its utility for constructing detailed, anatomically-informed models of brain function. In contrast, our analyses reproduce known neuroanatomy with precision and accuracy. This advantage is partly due to data acquisition procedures: while many DTI protocols measure diffusion in a small number of directions (e.g., 6 or 12), we employ a diffusion spectrum imaging (DSI)1, 2 protocol which assesses diffusion in 257 directions and at a range of magnetic gradient strengths. Moreover, DSI data allow us to use more sophisticated methods for reconstructing acquired data. In two experiments (visual attention and face perception), tractography reveals that co-active areas of the human brain are anatomically connected, supporting extant hypotheses that they form functional networks. DWI allows us to create a "circuit diagram" and reproduce it on an individual-subject basis, for the purpose of monitoring task-relevant brain activity in networks of interest.

We describe a novel approach for simultaneous analysis of brain function and structure using magnetic resonance imaging (MRI). We assess brain structure with high-resolution diffusion-weighted imaging and white-matter fiber tractography. Unlike standard structural MRI, these techniques allow us to directly relate anatomical connectivity to functional properties of brain networks.

The study of complex computational systems is facilitated by network maps, such as circuit diagrams. Such mapping is particularly informative when ...

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 ...

Extracting Visual Evoked Potentials from EEG Data Recorded During fMRI-guided Transcranial Magnetic Stimulation

Transcranial Magnetic Stimulation (TMS) is an effective method for establishing a causal link between a cortical area and cognitive/neurophysiological effects. Specifically, by creating a transient interference with the normal activity of a target region and measuring changes in an electrophysiological signal, we can establish a causal link between the stimulated brain area or network and the electrophysiological signal that we record. If target brain areas are functionally defined with prior fMRI scan, TMS could be used to link the fMRI activations with evoked potentials recorded. However, conducting such experiments presents significant technical challenges given the high amplitude artifacts introduced into the EEG signal by the magnetic pulse, and the difficulty to successfully target areas that were functionally defined by fMRI. Here we describe a methodology for combining these three common tools: TMS, EEG, and fMRI. We explain how to guide the stimulator&#39;s coil to the desired target area using anatomical or functional MRI data, how to record EEG during concurrent TMS, how to design an ERP study suitable for EEG-TMS combination and how to extract reliable ERP from the recorded data. We will provide representative results from a previously published study, in which fMRI-guided TMS was used concurrently with EEG to show that the face-selective N1 and the body-selective N1 component of the ERP are associated with distinct neural networks in extrastriate cortex. This method allows us to combine the high spatial resolution of fMRI with the high temporal resolution of TMS and EEG and therefore obtain a comprehensive understanding of the neural basis of various cognitive processes.

This paper describes a method for collecting and analyzing electroencephalography (EEG) data during concurrent transcranial magnetic stimulation (TMS) guided by activations revealed with functional magnetic resonance imaging (fMRI). A method for TMS artifact removal and extraction of event related potentials is described as well as considerations in paradigm design and experimental setup.

Transcranial Magnetic Stimulation (TMS) is an effective method for establishing a causal link between a cortical area and cognitive/neurophysiological ...

Deep Brain Stimulation with Simultaneous fMRI in Rodents

In order to visualize the global and downstream neuronal responses to deep brain stimulation (DBS) at various targets, we have developed a protocol for using blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) to image rodents with simultaneous DBS. DBS fMRI presents a number of technical challenges, including accuracy of electrode implantation, MR artifacts created by the electrode, choice of anesthesia and paralytic to minimize any neuronal effects while simultaneously eliminating animal motion, and maintenance of physiological parameters, deviation from which can confound the BOLD signal.&#160;Our laboratory has developed a set of procedures that are capable of overcoming most of these possible issues. For electrical stimulation, a homemade tungsten bipolar microelectrode is used, inserted stereotactically at the stimulation site in the anesthetized subject. In preparation for imaging, rodents are fixed on a plastic headpiece and transferred to the magnet bore. For sedation and paralysis during scanning, a cocktail of dexmedetomidine and pancuronium is continuously infused, along with a minimal dose of isoflurane; this preparation minimizes the BOLD ceiling effect of volatile anesthetics. In this example experiment, stimulation of the subthalamic nucleus (STN) produces BOLD responses which are observed primarily in ipsilateral cortical regions, centered in motor cortex. Simultaneous DBS and fMRI allows the unambiguous modulation of neural circuits dependent on stimulation location and stimulation parameters, and permits observation of neuronal modulations free of regional bias. This technique may be used to explore the downstream effects of modulating neural circuitry at nearly any brain region, with implications for both experimental and clinical DBS.

This protocol describes a standard method for simultaneous functional magnetic resonance imaging and deep brain stimulation in the rodent. The combined use of these experimental tools allows for the exploration of global downstream activity in response to electrical stimulation at virtually any brain target.

In order to visualize the global and downstream neuronal responses to deep brain stimulation (DBS) at various targets, we have developed a protocol for ...

Using Linear Agarose Channels to Study Drosophila Larval Crawling Behavior

Drosophila larval crawling is emerging as a powerful model to study neural control of sensorimotor behavior. However, larval crawling behavior on flat open surfaces is complex,&#160;including: pausing, turning, and meandering. This complexity in the repertoire of movement hinders detailed analysis of the events occurring during a single crawl stride cycle. To overcome this obstacle, linear agarose channels were made that constrain larval behavior to straight, sustained, rhythmic crawling. In principle, because agarose channels and the Drosophila larval body are both optically clear, the movement of larval structures labeled by genetically-encoded fluorescent probes can be monitored in intact, freely-moving larvae. In the past, larvae were placed in linear channels and crawling at the level of whole organism, segment, and muscle were analyzed1. In the future, larvae crawling in channels can be used for calcium imaging to monitor neuronal activity. Moreover, these methods can be used with larvae of any genotype and with any researcher-designed channel. Thus the protocol presented below is widely applicable for studies using the Drosophila larva as a model to understand motor control.

Using Linear Agarose Channels to Study Drosophila Larval Crawling Behavior

The Drosophila larva is a powerful model system to study neural control of behavior. This publication describes the use of linear agarose channels to elicit sustained bouts of linear crawling and methods to quantify the dynamics of larval structures during repetitive crawling behavior.

Drosophila larval crawling is emerging as a powerful model to study neural control of sensorimotor behavior. However, larval crawling behavior on flat ...

Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels

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Chapters in this video

Functional Mapping with Simultaneous MEG and EEG

Multielectrode Array Recordings of the Vomeronasal Epithelium

Simultaneous fMRI and Electrophysiology in the Rodent Brain

Combining Transcranial Magnetic Stimulation and fMRI to Examine the Default Mode Network

Electrophysiological Measurements and Analysis of Nociception in Human Infants

Co-analysis of Brain Structure and Function using fMRI and Diffusion-weighted Imaging

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

Extracting Visual Evoked Potentials from EEG Data Recorded During fMRI-guided Transcranial Magnetic Stimulation

Deep Brain Stimulation with Simultaneous fMRI in Rodents

Using Linear Agarose Channels to Study Drosophila Larval Crawling Behavior