The authors are thankful to the Coordination for the Improvement of Higher Education Personnel (CAPES) - Finance Code 001 and the Federal University of ABC (UFABC). Jo&#227;o R. Sato received financial support from the S&#227;o Paulo Research Foundation (FAPESP, Grants Nos. 2018/21934-5, 2018/04654-9, and 2023/02538-0).

Real-Time Recording and Mapping of Human Interaction with 3D Virtual Objects

The authors have no conflicts of interest to disclose.

As previously stated, this paper aims to present a detailed procedure of real-time mapping of fixation and saccade motion data on interactive 3D objects, which is easily customizable and only uses software available for free, providing step-by-step instructions to make everything work.
While this experimental setup involved a highly interactive task, such as moving a 3D object to match another object&#39;s orientation with PR in two of the three possible axes, we ensured thorough documentation...

Mental rotation (MR) is a cognitive ability that enables individuals to mentally manipulate and rotate objects, facilitating a better understanding of their features and spatial relationships. It is one of the visuospatial abilities, a fundamental cognitive group that was studied as early as 18901. Visuospatial abilities are an important component of an individual&#39;s cognitive repertoire that is influenced by both inherited and environmental factors2,3,4,5. Interest in visuospatial abilities has grown throughout the twentieth century due to mounting evidence of their importance in key subjects such as aging6 and development7, performance in science, technology, engineering, and mathematics (STEM)8,9, creativity10, and evolutionary traits11.
The contemporary idea of MR derives from the pioneering work published by Shepard and Metzler (SM) in 197112. They devised a chronometric method using a series of &#34;same or different&#34; tasks, presenting two projections of abstract 3D objects displayed side by side. Participants had to mentally rotate the objects on some axis and decide if those projections portrayed the same object rotated differently or distinct objects. The study revealed a positive linear correlation between response time (RT) and the angular disparity (AD) between representations of the same object. This correlation is known as the angle disparity effect (ADE). ADE is regarded as a behavioral manifestation of MR and became ubiquitous in several influential subsequent studies in the field13,14,15,16,17,18,19,20,21,22,23,24,25. The 3D objects employed in the SM study were composed of 10 contiguous cubes generated by the computer graph pioneer Michael Noll at Bell Laboratories26. They are referred to as SM figures and are widely employed in MR studies.
Two advancements were of great importance in Shepard and Metzler&#39;s seminal work; first, considering the contributions in the field of MR assessments. In 1978, Vanderberg and Kuze27 developed a psychometric 20-item pencil-and-paper test based on SM &#34;same or different&#34; figures that became known as the mental rotation test (VKMRT). Each test item presents a target stimulus. Participants must select among four stimuli, which ones represent the same object depicted in the target stimulus, and which do not. VKMRT has been used to investigate the correlation between MR ability and various other factors, such as sex-related differences6,21,24,28,29,30, aging and development6,31,32, academic performance8,33, and skills in music and sports34. In 1995, Peters et al. published a study with redrawn figures for the VKMRT35,36. Similarly, following the &#34;same or different&#34; task design, a variety of other libraries of computer-generated stimuli have been employed to investigate MR processes and to assess MR abilities (3D versions of the original SM stimuli19,22,23,37,38, human body mimicking SM figures25,39,40, flat polygons for 2D rotation41,42, anatomy, and organs43, organic shapes44, molecules45,46, among others21). The Purdue Spatial Visualization Test (PSVT) proposed by Guay in 197647 is also relevant. It entails a battery of tests, including MR (PSVT:R). Employing different stimuli from those in VKMRT, PSVT:R requires participants to identify a rotation operation in a model stimulus and mentally apply it to a different one. PSVT:R is also widely used, particularly in studies investigating the role of MR in STEM achievement48,49,50.
The second advancement of great importance in Shepard and Metzler&#39;s seminal work comprises the contributions to the understanding of the MR process, in particular, with the use of eye-tracking devices. In 1976, Just and Carpenter14 used analog video-based eye-tracking equipment to conduct a study based on Shepard and Metzler&#39;s ADE experiment. From their results on saccadic eye movements and RTs, they proposed a model of MR processes consisting of three phases: 1) the search phase, in which similar parts of the figures are recognized; 2) the transformation and comparison phase, in which one of the identified parts is mentally rotated; 3) the confirmation phase, in which it is decided whether the figures are the same or not. The phases are repeated recursively until a decision can be made. Each step corresponds to specific saccadic and fixational eye movement patterns in close relation to observed ADEs. Thus, by correlating eye activity to chronometric data, Just and Carpenter provided a cognitive signature for the study of MR processes. To date, this model, albeit with adaptations, has been adopted in several studies15,42,46,51,52,53.
Following this track, several ensuing studies monitoring behavioral18,19,22,23,25,34,40,54,55 and brain activity20,22,56,57 functions during stimuli rotation were conducted. Their findings point to a cooperative role between MR and motor processes. Moreover, there is a growing interest in investigating problem-solving strategies involving MR in relation to individual differences 15,41,46,51,58.
Overall, it can be considered that the design of studies aiming at understanding MR processes is based on presenting a task with visual stimuli that requests participants to perform an MR operation that, in turn, entails a motor reaction. If this reaction allows rotation of the stimuli, it is often called physical rotation (PR). Depending on the specific objectives of each study, different strategies and devices have been employed for data acquisition and analysis of MR and PR. In the task stimulus presentation step, it is possible to change the types of stimuli (i.e., previously cited examples); the projection (computer-generated images in traditional displays22,23,25,29,40,41,59, as well as in stereoscopes19 and virtual60 and mixed43 reality environments); and the interactivity of the stimuli (static images12,27,36, animations61, and interactive virtual objects19,22,23,43,53,59).
MR is usually inferred from measures of RTs (ADE), as well as ocular and brain activity25,46,62. Ocular activity is measured using eye-tracking data consisting of saccadic movements and fixations14,15,42,51,52,54,58,60, as well as pupillometry40. RT data typically arise from motor response data recorded while operating various devices such as levers13, buttons and switches14,53, pedals53, rotary knobs19, joysticks37, keyboard61 and mouse29,58,60, drive wheels53, inertial sensors22,23, touch screens52,59, and microphones22. To measure PR, in addition to the RTs, the study design will also include recording manual rotations of interactive stimuli while participants perform the MR task22,23,52,53.
In 1998, Wohlschl&#228;ger and Wohlschl&#228;ger19 used &#34;same or different&#34; tasks with interactive virtual SM stimuli manipulated with a knob, with rotations limited to one axis per task. They measured RT and the cumulative record of physical rotations performed during the tasks. Comparing situations with and without actual rotation of the interactive stimuli, they concluded that MR and PR share a common process for both imagined and actually performed rotations.
In 2014, two studies were conducted employing the same type of tasks with virtual interactive stimuli22,23. However, the objects were manipulated with inertial sensors that captured motion in 3D space. In both cases, in addition to RTs, rotation trajectories were recorded - the evolution of rotation differences between reference and interactive stimuli during the tasks. From these trajectories, it was possible to extract both cumulative information (i.e., the total number of rotations, in quaternionic units) and detailed information about solution strategies. Adams et al.23 studied the cooperative effect between MR and PR. In addition to RTs, they used the integral of the rotation trajectories as a parameter of accuracy and objectivity of resolution. Curve profiles were interpreted according to a three-step model63 (planning, major rotation, fine adjustment). The results indicate that MR and PR do not necessarily have a single, common factor. Gardony et al.22 collected data on RT, accuracy, and real-time rotation. In addition to confirming the relationship between MR and PR, the analysis of rotation trajectories revealed that participants manipulated the figures until they could identify whether they were different or not. If they were the same, participants would rotate them until they looked the same.
Continuing this strategy, in 2018, Wetzel and Bertel52 also used interactive SM figures in &#34;same or different&#34; tasks using touchscreen tablets as the interface. In addition, they used an eye-tracking device to obtain cumulative data on fixation time and saccadic amplitude as parameters of the cognitive load involved in solving MR tasks. The authors confirmed the previous studies discussed above regarding the relationships between MR and PR and the task-solving processes. However, in this study, they did not use fixation mapping and saccades data for the stimuli.
Methodological approaches for mapping eye-tracking data over virtual 3D objects have been proposed and constantly improved, commonly by researchers interested in studying the factors related to visual attention in virtual environments64. Although affordable and using similar eye-tracking devices, apparently, these methods have not been effectively integrated into the experimental repertoire employed in mental rotation studies with interactive 3D objects such as those previously mentioned. Conversely, we did not find any studies in the literature reporting real-time mapping of fixation and saccade motion data on interactive 3D objects. There seems to be no convenient method to integrate eye-activity data with rotation trajectories easily. In this research, we aim to contribute to filling this gap. The procedure is presented in detail, from data acquisition to graphical output generation.
In this paper, we describe in detail a method for studying mental rotation processes with virtual interactive 3D objects. The following advances are highlighted. First, it integrates quantitative behavioral motor (hand-driven object rotation via a computer interface) and ocular (eye-tracking) data collection during interaction sessions with 3D virtual models. Second, it requires only conventional computer equipment and eye-tracking devices for visual task design, data acquisition, recording, and processing. Third, it easily generates graphical output to facilitate data analysis - angular disparity, physical rotation, quaternionic rotation trajectories, and hit mapping of eye-tracking data over 3D virtual objects. Finally, the method requires only free software. All developed code and scripts are available free of charge (https://github.com/rodrigocnstest/rodrigocnstest.github.io).

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Firefox</td>
			<td>Mozilla Foundation (Open Source)</td>
			<td></td>
			<td>Any updated modern browser that is compatible with WebGL (https://caniuse.com/webgl), and in turn with Jmol, can be used</td>
		</tr>
		<tr>
			<td>GNU Octave</td>
			<td>Open Source</td>
			<td></td>
			<td>https://octave.org/</td>
		</tr>
		<tr>
			<td>Google Apps Script</td>
			<td>Google LLC</td>
			<td></td>
			<td>script.google.com</td>
		</tr>
		<tr>
			<td>Google Sheets</td>
			<td>Google LLC</td>
			<td></td>
			<td>https://www.google.com/sheets/about/</td>
		</tr>
		<tr>
			<td>Laptop</td>
			<td></td>
			<td></td>
			<td>Any computer that can run the eye tracking system software.</td>
		</tr>
		<tr>
			<td>Mangold Software Suite</td>
			<td>Mangold&#160;</td>
			<td></td>
			<td>Software interface used for the Eye tracking device. Any Software that outputs the data with system time values can be used.</td>
		</tr>
		<tr>
			<td>Mouse</td>
			<td></td>
			<td></td>
			<td>Any mouse capable of clicking and dragging with simple movements should be compatible. Human interfaces analogous to a mouse with the same capabilities, such as a touchscreen or pointer, should be compatible, but may behave differently.</td>
		</tr>
		<tr>
			<td>Vt3mini</td>
			<td>EyeTech Digital Systems</td>
			<td></td>
			<td>60 Hz. Any working Eye Tracking device should be compatible.</td>
		</tr>
	</tbody>
</table>

three-dimensional mapping of the rotation of interactive virtual objects with eye-tracking data

We present a method for real-time recording of human interaction with three-dimensional (3D) virtual objects. The approach consists of associating rotation data of the manipulated object with behavioral measures, such as eye tracking, to make better inferences about the underlying cognitive processes.
The task consists of displaying two identical models of the same 3D object (a molecule), presented on a computer screen: a rotating, interactive object (iObj) and a static, target object (tObj). Participants must rotate iObj using the mouse until they consider its orientation to be identical to that of tObj. The computer tracks all interaction data in real time. The participant&#39;s gaze data are also recorded using an eye tracker. The measurement frequency is 10 Hz on the computer and 60 Hz on the eye tracker.
The orientation data of iObj with respect to tObj are recorded in rotation quaternions. The gaze data are synchronized to the orientation of iObj and referenced using this same system. This method enables us to obtain the following visualizations of the human interaction process with iObj and tObj: (1) angular disparity synchronized with other time-dependent data; (2) 3D rotation trajectory inside what we decided to call a &#34;ball of rotations&#34;; (3) 3D fixation heatmap. All steps of the protocol have used free software, such as GNU Octave and Jmol, and all scripts are available as supplementary material.
With this approach, we can conduct detailed quantitative studies of the task-solving process involving mental or physical rotations, rather than only the outcome reached. It is possible to measure precisely how important each part of the 3D models is for the participant in solving tasks, and thus relate the models to relevant variables such as the characteristics of the objects, cognitive abilities of the individuals, and the characteristics of human-machine interface.

Evolution of angular disparity and other variables 
As depicted in step 3.3.1 in Supplemental File 2, two canvases are presented to the participant on the video monitor screen, displaying copies of the same 3D virtual object in different orientations. On the left canvas, the target object (tObj) remains static and serves as the target position or tObj position. On the right canvas, the interactive object (iObj) is shown in a different position and allows the partici...

Author Spotlight: Insights into the Analysis of Human Interaction with 3D Virtual Objects

We have developed a simple, customizable, and efficient method for recording quantitative processual data from interactive spatial tasks and mapping these rotation data with eye-tracking data.

Three-Dimensional Mapping of the Rotation of Interactive Virtual Objects with Eye-Tracking Data

We present a method for real-time recording of human interaction with three-dimensional (3D) virtual objects. The approach consists of associating ...

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816 Views.  University of São Paulo, Institute of Chemistry. We have developed a simple, customizable, and efficient method for recording quantitative processual data from interactive spatial tasks and mapping these rotation data with eye-tracking data.

Video: Author Spotlight: Insights into the Analysis of Human Interaction with 3D Virtual Objects

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 ...

Brain Imaging Investigation of the Neural Correlates of Observing Virtual Social Interactions

The ability to gauge social interactions is crucial in the assessment of others&#x2019; intentions. Factors such as facial expressions and body language affect our decisions in personal and professional life alike 1. These "friend or foe" judgements are often based on first impressions, which in turn may affect our decisions to "approach or avoid". Previous studies investigating the neural correlates of social cognition tended to use static facial stimuli 2. Here, we illustrate an experimental design in which whole-body animated characters were used in conjunction with functional magnetic resonance imaging (fMRI) recordings. Fifteen participants were presented with short movie-clips of guest-host interactions in a business setting, while fMRI data were recorded; at the end of each movie, participants also provided ratings of the host behaviour. This design mimics more closely real-life situations, and hence may contribute to better understanding of the neural mechanisms of social interactions in healthy behaviour, and to gaining insight into possible causes of deficits in social behaviour in such clinical conditions as social anxiety and autism 3.

This article demonstrates an experimental design in which whole-body animated characters are used in conjunction with functional magnetic resonance imaging (fMRI) to investigate the neural correlates of observing virtual social interactions.

The ability to gauge social interactions is crucial in the assessment of others&#x2019; intentions. Factors such as facial expressions and body language ...

Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury

After brain stroke microglia/macrophages (M/M) undergo rapid activation with dramatic morphological and phenotypic changes that include expression of novel surface antigens and production of mediators that build up and maintain the inflammatory response. Emerging evidence indicates that M/M are highly plastic cells that can assume classic pro-inflammatory (M1) or alternative anti-inflammatory (M2) activation after acute brain injury. However a complete characterization of M/M phenotype marker expression, their colocalization and temporal evolution in the injured brain is still missing.	
	Immunofluorescence protocols specifically staining relevant markers of M/M activation can be performed in the ischemic brain. Here we present immunofluorescence-based protocols followed by three-dimensional confocal analysis as a powerful approach to investigate the pattern of localization and co-expression of M/M phenotype markers such as CD11b, CD68, Ym1, in mouse model of focal ischemia induced by permanent occlusion of the middle cerebral artery (pMCAO). Two-dimensional analysis of the stained area reveals that each marker is associated to a defined M/M morphology and has a given localization in the ischemic lesion. Patterns of M/M phenotype marker co-expression can be assessed by three-dimensional confocal imaging in the ischemic area. Images can be acquired over a defined volume (10 &mu;m z-axis and a 0.23 &mu;m step size, corresponding to a 180 x 135 x 10 &mu;m volume) with a sequential scanning mode to minimize bleed-through effects and avoid wavelength overlapping. Images are then processed to obtain three-dimensional renderings by means of Imaris software. Solid view of three dimensional renderings allows the definition of marker expression in clusters of cells. We show that M/M have the ability to differentiate towards a multitude of phenotypes, depending on the location in the lesion site and time after injury.

A way to gain new insights into the complexity of the brain inflammatory response is presented. We describe immunofluorescence-based protocols followed by three-dimensional confocal analysis to investigate the pattern of co-expression of microglia/macrophage phenotype markers in a mouse model of focal ischemia.

After brain stroke microglia/macrophages (M/M) undergo  rapid activation with dramatic morphological and phenotypic changes that  include expression of ...

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify their functional and structural properties, a condition called reactive astrogliosis. Here, a protocol for assessment of the morphological properties of astrocytes is presented. This protocol includes quantification of 12 different parameters i.e. the surface area and volume of the tissue covered by an astrocyte (astrocyte territory), the entire astrocyte including branches, cell body, and nucleus, as well as total length and number of branches, the intensity of fluorescence immunoreactivity of antibodies used for astrocyte detection, and astrocyte density (number/1,000 &#181;m2). For this purpose three-dimensional (3D) confocal microscopic images were created, and 3D image analysis software such as Volocity 6.3 was used for measurements. Rat brain tissue exposed to amyloid beta1-40 (A&#946;1-40) with or without a therapeutic&#160;intervention was used to present the method. This protocol can also be used for 3D morphometric analysis of other cells from either in vivo or in vitro conditions.

Astrocytes in the CNS change their functional and structural properties in response to harmful stimuli. This report presents a protocol for assessment of three-dimensional astrocyte morphology in diseased conditions or after therapeutic interventions.

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify ...

Three-dimensional Imaging and Analysis of Mitochondria within Human Intraepidermal Nerve Fibers

The goal of this protocol is to study mitochondria within intraepidermal nerve fibers. Therefore, 3D imaging and analysis techniques were developed to isolate nerve-specific mitochondria and evaluate disease-induced alterations of mitochondria in the distal tip of sensory nerves. The protocol combines fluorescence immunohistochemistry, confocal microscopy and 3D image analysis techniques to visualize and quantify nerve-specific mitochondria. Detailed parameters are defined throughout the procedures in order to provide a concrete example of how to use these techniques to isolate nerve-specific mitochondria. Antibodies were used to label nerve and mitochondrial signals within tissue sections of skin punch biopsies, which was followed by indirect immunofluorescence to visualize nerves and mitochondria with a green and red fluorescent signal respectively. Z-series images were acquired with confocal microscopy and 3D analysis software was used to process and analyze the signals. It is not necessary to follow the exact parameters described within, but it is important to be consistent with the ones chosen throughout the staining, acquisition and analysis steps. The strength of this protocol is that it is applicable to a wide variety of circumstances where one fluorescent signal is used to isolate other signals that would otherwise be impossible to study alone.

This protocol uses three-dimensional (3D) imaging and analysis techniques to visualize and quantify nerve-specific mitochondria. The techniques are applicable to other situations where one fluorescent signal is used to isolate a subset of data from another fluorescent signal.

The goal of this protocol is to study mitochondria within intraepidermal nerve fibers. Therefore, 3D imaging and analysis techniques were developed to ...

Fiber Connections of the Supplementary Motor Area Revisited: Methodology of Fiber Dissection, DTI, and Three Dimensional Documentation

The purpose of this study is to show the methodology for the examination of the white matter connections of the supplementary motor area (SMA) complex (pre-SMA and SMA proper) using a combination of fiber dissection techniques on cadaveric specimens and magnetic resonance (MR) tractography. The protocol will also describe the procedure for a white matter dissection of a human brain, diffusion tensor tractography imaging, and three-dimensional documentation. The fiber dissections on human brains and the 3D documentation were performed at the University of Minnesota, Microsurgery and Neuroanatomy Laboratory, Department of Neurosurgery. Five postmortem human brain specimens and two whole heads were prepared in accordance with Klingler's method. Brain hemispheres were dissected step by step from lateral to medial and medial to lateral under an operating microscope, and 3D images were captured at every stage. All dissection results were supported by diffusion tensor imaging. Investigations on the connections in line with Meynert's fiber tract classification, including association fibers (short, superior longitudinal fasciculus I and frontal aslant tracts), projection fibers (corticospinal, claustrocortical, cingulum, and frontostriatal tracts), and commissural fibers (callosal fibers) were also conducted.

The purpose of this study is to show each step of the fiber dissection technique on human cadaveric brains, the 3D documentation of these dissections, and the diffusion tensor imaging of the anatomically dissected fiber pathways.

The purpose of this study is to show the methodology for the examination of the white matter connections of the supplementary motor area (SMA) complex ...

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical properties, synaptic connections, and in vivo functions, but their basic functional and anatomical organization from cellular to network scale is poorly understood. Here we describe a method for the three-dimensional imaging of fluorescently-labeled neurons across large areas of the brain for the investigation of the cortical cellular organization. Specific types of neurons are labeled by the injection of fluorescent retrograde neuronal tracers or expression of fluorescent proteins in transgenic mice. Block brain samples, e.g., a hemisphere, are prepared after fixation, made transparent with tissue clearing methods, and subjected to fluorescent immunolabeling of the specific cell types. Large areas are scanned using confocal or two-photon microscopes equipped with large working distance objectives and motorized stages. This method can resolve the periodic organization of the cell type-specific microcolumn functional modules in the mouse neocortex. The procedure can be useful for the study of three-dimensional cellular architecture in the diverse brain areas and other complex tissues.

Here we describe a procedure for tissue clearing, fluorescent labeling, and large-scale imaging of mouse brain tissue which, thereby, enables visualization of the three-dimensional organization of cell types in the neocortex.

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical ...

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. We have developed a software package for accurate and robust shape modeling and group-wise analysis. Here, we introduce an pipeline for the shape analysis, from individual 3D shape modeling to quantitative group shape analysis. We also describe the pre-processing and segmentation steps using open software packages. This practical guide would help researchers save time and effort in 3D shape analysis on brain structures.

We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images.

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. ...

Translational Brain Mapping at the University of Rochester Medical Center: Preserving the Mind Through Personalized Brain Mapping

The Translational Brain Mapping Program at the University of Rochester is an interdisciplinary effort that integrates cognitive science, neurophysiology, neuroanesthesia, and neurosurgery. Patients who have tumors or epileptogenic tissue in eloquent brain areas are studied preoperatively with functional and structural MRI, and intraoperatively with direct electrical stimulation mapping. Post-operative neural and cognitive outcome measures fuel basic science studies about the factors that mediate good versus poor outcome after surgery, and how brain mapping can be further optimized to ensure the best outcome for future patients. In this article, we describe the interdisciplinary workflow that allows our team to meet the synergistic goals of optimizing patient outcome and advancing scientific understanding of the human brain.

This article provides an overview of a multi-modal brain mapping program designed to identify regions of the brain that support critical cognitive functions in individual neurosurgery patients.

The Translational Brain Mapping Program at the University of Rochester is an interdisciplinary effort that integrates cognitive science, neurophysiology, ...

Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images (SDM-PSI)

Most methods for conducting meta-analysis of voxel-based neuroimaging studies do not assess whether effects are not null, but whether there is a convergence of peaks of statistical significance, and reduce the assessment of the evidence to a binary classification exclusively based on p-values (i.e., voxels can only be &ldquo;statistically significant&rdquo; or &ldquo;non-statistically significant&rdquo;). Here, we detail how to conduct a meta-analysis using Seed-based d Mapping with Permutation of Subject Images (SDM-PSI), a novel method that uses a standard permutation test to assess whether effects are not null. We also show how to grade the strength of the evidence according to a set of criteria that considers a range of statistical significance levels (from more liberal to more conservative), the amount of data or the detection of potential biases (e.g., small-study effect and excess of significance). To exemplify the procedure, we detail the conduction of a meta-analysis of voxel-based morphometry studies in obsessive-compulsive disorder, and we provide all the data already extracted from the manuscripts to allow the reader to replicate the meta-analysis easily. SDM-PSI can also be used for meta-analyses of functional magnetic resonance imaging, diffusion tensor imaging, position emission tomography and surface-based morphometry studies.

Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images SDM-PSI

We detail how to conduct a meta-analysis of voxel-based neuroimaging studies using Seed-based d Mapping with Permutation of Subject Images (SDM-PSI).