This work was supported by the National Institutes of Health [R01EY030996].

Research with human participants was performed in compliance with institutional guidelines at the University of Texas Health Science Center and Stony Brook University, with informed consent obtained from participants for these studies and use of their data.
1. Setup of MRI scanner and imaging protocols
<ol>
	<li>For fMRI, use a 3T MRI scanner with multi-channel receiver head coils. Different field strengths can also be used but may present difficulties with signal-to-noise ratio (SNR) or distortion artifacts, so adjust accordingly. Use only the posterior half of the head coil for fMRI to allow for a larger viewing angle unobstructed by the anterior half of the coil.</li>
	<li>Set up a T1-weighted magnetization-prepared rapid acquisition gradient echo (MP-RAGE) sequence with a repetition time (TR) of 2.2 s, echo time (TE) of 2.8 ms, field of view (FOV) of 176 mm x 256 mm x 208 mm, spatial resolution of 1 mm x 1 mm x 1 mm, bandwidth of 190 Hz/pixel, flip angle of 13&#176;, and a scan duration of 3.1 min3.</li>
	<li>Set up a gradient-echo, echo-planar imaging (EPI) sequence with a TR of 2 s, TE of 30 ms, FOV of 220 mm x 220 mm, in-plane resolution of 1.7 mm x 1.7 mm, 29 slices with a thickness of 3 mm, and a bandwidth of 1,500 Hz/pixel3.</li>
	<li>Measure the dimensions of the head coil and scanner bore, and then construct a simple frame by cutting a polyvinyl chloride (PVC) pipe into suitable lengths and connecting them with PVC elbows. Obtain a mirror that is at least 25 cm wide and 15 cm tall and attach it to a plastic rod with screws (small holes can be drilled into the mirror).
	<ol>
		<li>Attach the ends of the plastic rod to the PVC frame with nylon screws (Figure 1A). Make sure that the nylon screws are slightly loose to allow the mirror to be rotated by hand to optimize the angle for each participant.</li>
	</ol>
	</li>
	<li>Make a screen to go inside the MRI bore. Cut a segment of a rear-projection screen that is approximately the size of the MRI bore. Construct a frame that is the size of the bore and attach the screen to the frame with screws. Place the screen inside the scanner just behind the head coil to minimize the distance between the screen and mirror and maximize the FOV. 
	NOTE: If the scanner bore is large enough, a single screen can be used for the participant to view directly instead of the mirror and rear projection screen setup. A projection screen attached to a thin sheet of wood for backing or a sheet of thin matte white plastic can be used as a screen and placed on the frame instead of a mirror. The projector should then be positioned and focused, such that it fills the screen and is in focus.</li>
</ol>
2. Participant preparation
<ol>
	<li>Inform the participant about the procedure, risks, and benefits of the fMRI scan. Obtain their informed consent.</li>
	<li>Ensure that the participant does not have any contraindications to MRI. This includes screening for pacemakers, metal implants, or claustrophobia. If you have any uncertainty, consult with a qualified radiologist or researcher, and exclude the participant from the study if any uncertainty remains.</li>
	<li>Explain the visual stimulation protocol and the need for the participants to fixate on the central cross during the fMRI scans. Show the participant a short demonstration of the visual stimulation for instructional purposes to familiarize them with the procedure.</li>
	<li>Carefully position the participant on the table of the MRI scanner to ensure that they are comfortable and relaxed. Provide earplugs and/or a sound-dampening headset to reduce the acoustic noise the participant will hear to protect their hearing.</li>
	<li>Immobilize the participant&#39;s head in the posterior half of the head coil array, using foam padding on the sides of the head to ensure that the head is properly immobilized to reduce motion artifacts. Use the scanner&#39;s positioning system and move the table into the scanner bore.</li>
	<li>Place the wide-view screen or mirror 10 cm from the patient&#39;s eyes (Figure 1B). Place the bore-sized screen from the back of the scanner bore just behind the head coil. Adjust the position and angle of the mirror/screen for each participant to achieve a consistent viewing angle.</li>
	<li>Ensure that the participant is comfortable throughout the scan via communication through the intercom.</li>
</ol>
3. fMRI scanning of participant
<ol>
	<li>Run a localizer scan with three orthogonal planes and scanner adjustments and calibrations for frequency adjustment and shimming.</li>
	<li>Run an MP-RAGE anatomical scan to help position the EPI slices.</li>
	<li>Create visual stimuli, as described in the following steps, using a program for running behavioral or psychological experiments.</li>
	<li>At the start of the fMRI protocol, instruct the participant to fixate on the white cross (3&#176; x 3&#176;), which should be on top of a gray background at the center of the stimuli for 10 s. 
	NOTE: The white cross will be shown before and after each visual stimulation paradigm for 10 s. Thus, the total fMRI stimulation test for each paradigm is 200 s.</li>
	<li>Present the first visual stimulation paradigm (a series of rotating wedges) for a period of 30 s (giving an angular velocity of 6&#176;/s) and cycle through six periods. The wedge stimuli should include 12 frames of rotating wedges (one scan with clockwise rotation and one with counterclockwise), extending to the edge of the screen/mirror (&#62;100&#176; visual field), with an 8 Hz contrast-reversing black and white (100% contrast) checkerboard pattern (Figure 2A).</li>
	<li>Present the white cross once again for 10 s.</li>
	<li>Repeat steps 3.4-3.6 with the second visual stimulation paradigm (a series of expanding and contracting rings) for a period of 30 s (expanding or contracting at 1.8&#176;/s of the visual field) and cycle through six periods. The ring stimuli should include eight frames of expanding or contracting rings (&#62;100&#176; visual field), with an 8 Hz contrast-reversing black and white (100% contrast) checkerboard pattern (Figure 2B).</li>
	<li>After completing the fMRI, move the table out of the scanner bore while instructing the participant to remain still. Remove the mirror/screen, place the anterior portion of the head coil in addition to the posterior, and move the table back into the center of the scanner.</li>
	<li>Acquire a quick localizer scan in case of any movement and acquire an MP-RAGE scan with the full head coil. 
	NOTE: An anatomical image with the whole head coil is needed for accurate registration for group analyses and reconstruction purposes.</li>
</ol>
4. Analysis of retinotopic fMRI data
<ol>
	<li>Download and install the FreeSurfer application for MRI analysis (https://surfer.nmr.mgh.harvard.edu)20. 
	NOTE: FreeSurfer version 5.3.0 was used herein.</li>
	<li>Obtain images in Digital Imaging and Communications in Medicine (DICOM) format from the MRI scanner. Convert the DICOM files to nifti format using the dcm2niix application (https://www.nitrc.org/projects/mricrogl)21.</li>
	<li>Process the T1-weighted scan to provide a cortical surface reference, as described in the following two steps. Use FreeSurfer to convert structural data from nifti format to .mgz format (mri_convert command).</li>
	<li>Use the recon-all command in a shell environment to perform automated segmentation and cortical reconstruction of the structural data. 
	NOTE: This step can take over 20 h to complete.</li>
	<li>Use the graphical user interface tksurfer to view the inflated hemisphere and virtually cut the visual cortex along the calcarine fissure, and select the occipital lobe. Use the mris_flatten command to flatten the visual cortex patch. Repeat this step for both hemispheres.</li>
	<li>For the fMRI data, first remove the rest periods, with only the fixation cross presented, from the start and end of the data. Screen the fMRI data for artifacts or large movements.</li>
	<li>Preprocess the functional data for spatial smoothing and motion correction. Model the retinotopic stimulus paradigm and apply a canonical hemodynamic response function to construct the response function.</li>
	<li>Perform retinotopic phase-encoded analysis of the fMRI data using the FreeSurfer functional analysis stream (mkanalysis-sess, selxavg3-sess, and fieldsign-sess commands) to correlate the BOLD fMRI time series with a modeled response function and obtain phase-encoded retinotopic maps, with a significance level of p &#60; 0.01 (Figure 3).</li>
	<li>Visualize the results of the retinotopic maps with color-coded activation maps overlaid on the virtually flattened visual cortex using the tksurfer-sess command, and display using the rtview command.</li>
	<li>Use the phase-encoded retinotopic maps from the wedge stimuli to help define the boundaries of the primary visual cortex (V1) and other extra striate areas (V2 and V3) by field sign maps (Figure 3A), along with anatomical landmarks and FreeSurfer atlases.</li>
	<li>To calculate the BOLD response at different eccentricities, first use FSL Feat (http://fsl.fmrib.ox.ac.uk/fsl) to calculate statistical maps using a general linear model for each size of ring stimuli with a z-score threshold of Z &#62; 2.322,23. If group analysis is being performed, calculate the second level analysis for statistical maps of group differences with FSL Feat to help determine the BOLD response at different eccentricities.</li>
	<li>Co-register the fMRI images onto the reconstructed cortical surface using the FreeSurfer bbregister and tkregister2 commands to align the participant&#39;s fMRI data to the anatomical structural image of their brain and ensure accurate spatial alignment.</li>
	<li>Group the ring stimuli by eccentricity for each of the eight frames. Manually draw regions of interest for different eccentricities based on the activated voxel regions for each frame. Take the BOLD percent changes and plot them as a function of eccentricity. Also, bin the eccentricity data into central (&#60; &#177;12&#176;) and peripheral (&#62; &#177;12&#176;) regions, where a &#177;12&#176; visual stimulus is typical for retinotopic fMRI studies.</li>
</ol>

Advancing Visual Cortex Mapping for Enhanced Evaluation of Vision Disorders

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The authors have nothing to disclose.

The above protocol for utilization of wide-view retinotopic fMRI is an innovative method to evaluate the effects of vision loss and eye diseases on the brain. Through wide-field retinotopic mapping of the visual cortex with the use of a wider-view screen, this approach allows for a more comprehensive understanding of the visual system's functional organization. This could lead to a better understanding of abnormalities in the brain's visual processing system, which occurs in neurodegeneration, such as in glaucoma<sup cla...

Functional magnetic resonance imaging (fMRI) is a valuable method to assess changes in regional neurovascular function within the visual cortex in response to stimuli, as changes in regional blood flow correlate to the activation of brain regions1,2. High-resolution retinotopic blood oxygenation level-dependent (BOLD) signal measurements represent changes in deoxyhemoglobin, which are driven by localized changes in blood flow and blood oxygenation within the brain1,2. BOLD activity patterns collected from fMRI data can be used to functionally map the peripheral and central visual cortex, as well as detect changes in the retinotopic map in response to visual impairment and neurodegeneration3.
Most previous fMRI studies made use of narrow-view (around &#177;12&#176; of the central visual field) non-retinotopic stimuli or simple retinotopic stimuli with narrow-view visual stimuli, which provided limited functional parcellation of the retinotopic representation in the visual cortex and limited assessment to only the central visual field, excluding the periphery3. Consequently, narrow-view fMRI data has reported inconsistent BOLD percent changes in glaucoma patients4,5,6. There is therefore a need for improved fMRI approaches to assessing the peripheral and central visual field, particularly in the evaluation of diseases such as glaucoma.
Glaucoma is the leading cause of irreversible blindness, affecting 10% of people by the age of 807. Glaucoma is caused by the progressive, irreversible neurodegeneration of retinal ganglion cells, which are responsible for transmitting visual stimuli to the brain through the optic nerve. In primary open-angle glaucoma (POAG), the most common form of glaucoma, increased intraocular pressure causes thinning of the retinal nerve fiber layer (RNFL), leading to the loss of peripheral vision followed by peripheral and central blindess8,9,10,11. Histological evidence from animal studies suggests that glaucoma additionally results in progressive neurodegeneration of the optic nerve, optic tract, lateral geniculate nucleus, optic radiation, and visual cortex12,13. MRI technology offers a minimally invasive method of assessing both blood oxygenation and neurodegeneration in the visual cortex. In patients with glaucoma, MRI has found evidence of gray-matter atrophy in the visual pathway13,14,15,16 and abnormal white matter in the optic chiasm, optic tract, and optic radiation1,17,18.
To further explore the effects on visual processing, fMRI can be used to detect brain function in response to visual cues. The protocol herein describes a novel method to obtain a low-cost, wide-view retinotopic map using high-resolution retinotopy fMRI with wide-field (&#62;100&#176;) stimuli, as described by Zhou et al3. Visual stimuli of expanding rings and rotating wedges were used to elicit retinotopic mapping of the eccentricity and polar angle for fMRI. BOLD fMRI percent changes were analyzed as a function of eccentricity to evaluate brain function, corresponding to both central and peripheral vision. The BOLD fMRI percent change may be used to visualize activation throughout the visual cortex. These fMRI measures provide a reliable new method to evaluate neurodegenerative changes and their functional effects on the visual cortex found in eye diseases involving visual field defects, such as glaucoma.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1/4&#34;-20 nylon machine screws, knurled head thumb screw</td>
			<td></td>
			<td></td>
			<td>to attach rod to PVC frame</td>
		</tr>
		<tr>
			<td>1-1/4 inch PVC pipe</td>
			<td></td>
			<td></td>
			<td>length of ~5-10 ft is needed</td>
		</tr>
		<tr>
			<td>3T MRI scanner</td>
			<td>Siemens</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>6-32 nylon machine screws, rounded head</td>
			<td></td>
			<td></td>
			<td>to attach mirror/screen to rod</td>
		</tr>
		<tr>
			<td>8-channel head array coil</td>
			<td>Siemens</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>90 degree PVC elbow, 1-1/4 inch fitting</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Acrylic mirror</td>
			<td></td>
			<td></td>
			<td>Width and length of 25-30cm</td>
		</tr>
		<tr>
			<td>Acrylic rod</td>
			<td></td>
			<td></td>
			<td>1 inch width, ~ 2 ft long depening on size of scanner bore and head coil</td>
		</tr>
		<tr>
			<td>E-Prime</td>
			<td>Psychology Software Tools</td>
			<td></td>
			<td>to prepare and present visual stimuli paradigms</td>
		</tr>
		<tr>
			<td>Plywood sheet, 1/2 inch thick</td>
			<td></td>
			<td></td>
			<td>Size should be at least as large as the scanner bore. Cut as bore-sized frame for the projection screen</td>
		</tr>
		<tr>
			<td>Rear projection screen</td>
			<td></td>
			<td></td>
			<td>Size should be at least as large as the scanner bore</td>
		</tr>
	</tbody>
</table>

functional magnetic resonance imaging (fmri) of the visual cortex with wide-view retinotopic stimulation

High-resolution retinotopic blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) with a wide-view presentation can be used to functionally map the peripheral and central visual cortex. This method for measuring functional changes of the visual brain allows for functional mapping of the occipital lobe, stimulating &gt;100&#176; (&plusmn;50&#176;) or more of the visual field, compared to standard fMRI visual presentation setups which usually cover &lt;30&#176; of the visual field. A simple wide-view stimulation system for BOLD fMRI can be set up using common MR-compatible projectors by placing a large mirror or screen close to the subject's face and using only the posterior half of a standard head coil to provide a wide-viewing angle without obstructing their vision. The wide-view retinotopic fMRI map can then be imaged using various retinotopic stimulation paradigms, and the data can be analyzed to determine the functional activity of visual cortical regions corresponding to central and peripheral vision. This method provides a practical, easy-to-implement visual presentation system that can be used to evaluate changes in the peripheral and central visual cortex due to eye diseases such as glaucoma and the vision loss that may accompany them.

Nine participants diagnosed with POAG (four males, 36-74 years old) and nine age-matched healthy volunteers (six males, 53-65) were evaluated using the aforementioned wide-view fMRI protocol, as previously described by Zhou et al3. POAG was confirmed clinically in patients with an open angle by assessment of the presentation of visual field defects consistent with glaucoma, optic disc cupping, and/or an intraocular pressure (IOP) greater than 21 mmHg3. A wide-view visual pr...

Watch this Scientific Journal Video about Insights into Visual Cortex Research Through Wide-View fMRI Mapping at JoVE.com

Author Spotlight: Insights into Visual Cortex Research Through Wide-View fMRI Mapping 

We have developed techniques for mapping the visual cortex function utilizing more of the visual field than is commonly used. This approach has the potential to enhance the evaluation of vision disorders and eye diseases.

Functional Magnetic Resonance Imaging (fMRI) of the Visual Cortex with Wide-View Retinotopic Stimulation

High-resolution retinotopic blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) with a wide-view presentation can be ...

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Research

JoVE Journal

Neuroscience

1.3K Views.  Renaissance School of Medicine at Stony Brook University. We have developed techniques for mapping the visual cortex function utilizing more of the visual field than is commonly used. This approach has the potential to enhance the evaluation of vision disorders and eye diseases.

Video: Author Spotlight: Insights into Visual Cortex Research Through Wide-View fMRI Mapping 

Chronic Imaging of Mouse Visual Cortex Using a Thinned-skull Preparation

In vivo imaging using two-photon laser scanning microscopy (2PLSM) allows the study of living cells and neuronal processes in the intact brain. The technique presented here allows the imaging of the same area of the brain at several time points (chronic imaging) with microscopic resolution allowing the tracking of dendritic spines which are the small structures that represent the majority of postsynaptic excitatory sites in the CNS. The ability to clearly resolve fine cortical structures over several time points has many advantages, specifically in the study of brain plasticity in which morphological changes at synapses and circuit remodeling may help explain underlying mechanisms. In this video and supplementary material, we show a protocol for chronic in vivo imaging of the intact brain using a thinned-skull preparation. The thinned-skull preparation is a minimally invasive approach, which avoids potential damage to the dura and/or cortex, thus reducing the onset of an inflammatory response. When this protocol is performed correctly, it is possible to clearly monitor changes in dendritic spine characteristics in the intact brain over a prolonged period of time.

In this video and supplemental material, we show a protocol for chronic in vivo imaging of the intact brain using a thinned-skull preparation.

In vivo imaging using two-photon laser scanning microscopy (2PLSM) allows the study of living cells and neuronal processes in the intact brain. The ...

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 ...

State-Dependency Effects on TMS:  A Look at Motive Phosphene Behavior

Transcranial magnetic stimulation (TMS) is 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.1,2 Within the field of TMS, the term state dependency refers to the initial, baseline condition of the particular neural region targeted for stimulation. As can be inferred, the effects of TMS can (and do) vary according to this primary susceptibility and responsiveness of the targeted cortical area.3,4,5

In this experiment, we will examine this concept of state dependency through the elicitation and subjective experience of motive phosphenes. Phosphenes are visually perceived flashes of small lights triggered by electromagnetic pulses to the visual cortex. These small lights can assume varied characteristics depending upon which type of visual cortex is being stimulated. In this particular study, we will be targeting motive phosphenes as elicited through the stimulation of V1/V2 and the V5/MT+ complex visual regions.6

In this article, we examine the effects of visually relevant state dependency on TMS induced motive phosphenic presentations.

Transcranial magnetic stimulation (TMS) is a non-invasive neurostimulatory and neuromodulatory technique that can transiently or lastingly modulate ...

Multiple-mouse Neuroanatomical Magnetic Resonance Imaging

The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and evaluating mouse models of human disease. MRI is an excellent modality for investigating genetically altered animals. It is capable of whole brain coverage, can be used in vivo, and provides multiple contrast mechanisms for investigating different aspects of neuranatomy and physiology. The advent of high-field scanners along with the ability to scan multiple mice simultaneously allows for rapid phenotyping of novel mutations.
Effective mouse MRI studies require attention to many aspects of experiment design. In this article, we will describe general methods to acquire quality images for mouse phenotyping using a system that images mice concurrently in shielded transmit/receive radio frequency (RF) coils in a common magnet (Bock et al., 2003). We focus particularly on anatomical phenotyping, an important and accessible application that has shown a high potential for impact in many mouse models at our imaging centre. Before we can provide the detailed steps to acquire such images, there are important practical considerations for both in vivo brain imaging (Dazai et al., 2004) and ex vivo brain imaging (Spring et al., 2007) that should be noted. These are discussed below.

Magnetic resonance imaging (MRI) has become an increasingly popular tool for examining the phenotype of genetically altered mice. This article illustrates the methods necessary to achieve high-throughput phenotyping of genetically altered mice using multiple-mouse MRI.

The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and ...

High-resolution Functional Magnetic Resonance Imaging Methods for Human Midbrain

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon measuring activity on the surface of cerebral cortex rather than in subcortical regions such as midbrain and brainstem. Subcortical fMRI must overcome two challenges: spatial resolution and physiological noise. Here we describe an optimized set of techniques developed to perform high-resolution fMRI in human SC, a structure on the dorsal surface of the midbrain; the methods can also be used to image other brainstem and subcortical structures.
High-resolution (1.2 mm voxels) fMRI of the SC requires a non-conventional approach. The desired spatial sampling is obtained using a multi-shot (interleaved) spiral acquisition1. Since, T2* of SC tissue is longer than in cortex, a correspondingly longer echo time (TE ~ 40 msec) is used to maximize functional contrast. To cover the full extent of the SC, 8-10 slices are obtained. For each session a structural anatomy with the same slice prescription as the fMRI is also obtained, which is used to align the functional data to a high-resolution reference volume.
In a separate session, for each subject, we create a high-resolution (0.7 mm sampling) reference volume using a T1-weighted sequence that gives good tissue contrast. In the reference volume, the midbrain region is segmented using the ITK-SNAP software application2. This segmentation is used to create a 3D surface representation of the midbrain that is both smooth and accurate3. The surface vertices and normals are used to create a map of depth from the midbrain surface within the tissue4.
Functional data is transformed into the coordinate system of the segmented reference volume. Depth associations of the voxels enable the averaging of fMRI time series data within specified depth ranges to improve signal quality. Data is rendered on the 3D surface for visualization.
In our lab we use this technique for measuring topographic maps of visual stimulation and covert and overt visual attention within the SC1. As an example, we demonstrate the topographic representation of polar angle to visual stimulation in SC.

This article describes techniques to perform high-resolution functional magnetic resonance imaging with 1.2 mm sampling in human midbrain and subcortical structures using a 3T scanner. Use of these techniques to resolve topographic maps of visual stimulation in the human superior colliculus (SC) is given as an example.

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon ...

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 ...

The Use of Magnetic Resonance Spectroscopy as a Tool for the Measurement of Bi-hemispheric Transcranial Electric Stimulation Effects on Primary Motor Cortex Metabolism

Transcranial direct current stimulation (tDCS) is a neuromodulation technique that has been increasingly used over the past decade in the treatment of neurological and psychiatric disorders such as stroke and depression. Yet, the mechanisms underlying its ability to modulate brain excitability to improve clinical symptoms remains poorly understood 33. To help improve this understanding, proton magnetic resonance spectroscopy (1H-MRS) can be used as it allows the in vivo quantification of brain metabolites such as &#947;-aminobutyric acid (GABA) and glutamate in a region-specific manner 41. In fact, a recent study demonstrated that 1H-MRS is indeed a powerful means to better understand the effects of tDCS on neurotransmitter concentration 34. This article aims to describe the complete protocol for combining tDCS (NeuroConn MR compatible stimulator) with 1H-MRS at 3 T using a MEGA-PRESS sequence. We will describe the impact of a protocol that has shown great promise for the treatment of motor dysfunctions after stroke, which consists of bilateral stimulation of primary motor cortices 27,30,31. Methodological factors to consider and possible modifications to the protocol are also discussed.

This article aims to describe a basic protocol for combining transcranial direct current stimulation (tDCS) with proton magnetic resonance spectroscopy (1H-MRS) measurements to investigate the effects of bilateral stimulation on primary motor cortex metabolism.

Transcranial direct current stimulation (tDCS) is a neuromodulation technique that has been increasingly used over the past decade in the treatment of ...

Effects of Transcranial Alternating Current Stimulation on the Primary Motor Cortex by Online Combined Approach with Transcranial Magnetic Stimulation

Transcranial Alternating Current Stimulation (tACS) is a neuromodulatory technique able to act through sinusoidal electrical waveforms in a specific frequency and in turn modulate ongoing cortical oscillatory activity. This neurotool allows the establishment of a causal link between endogenous oscillatory activity and behavior. Most of the tACS studies have shown online effects of tACS. However, little is known about the underlying action mechanisms of this technique because of the AC-induced artifacts on Electroencephalography (EEG) signals. Here we show a unique approach to investigate online physiological frequency-specific effects of tACS of the primary motor cortex (M1) by using single pulse Transcranial Magnetic Stimulation (TMS) to probe cortical excitability changes. In our setup, the TMS coil is placed over the tACS electrode while Motor Evoked Potentials (MEPs) are collected to test the effects of the ongoing M1-tACS. So far, this approach has mainly been used to study the visual and motor systems. However, the current tACS-TMS setup can pave the way for future investigations of cognitive functions. Therefore, we provide a step-by-step manual and video guidelines for the procedure.

Transcranial Alternating Current Stimulation (tACS) allows the modulation of cortical excitability in a frequency-specific fashion. Here we show a unique approach which combines online tACS with single pulse Transcranial Magnetic Stimulation (TMS) in order to "probe" cortical excitability by means of Motor Evoked Potentials.

Transcranial Alternating Current Stimulation (tACS) is a neuromodulatory technique able to act through sinusoidal electrical waveforms in a specific ...