16.5: Course Readings and Materials
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Required Course Materials
The standard text for this course is: Biology of Aging The text is an open source textbook and available under the textbook tab at the top of this page. |
In this course you will be using conventional productivity software, such as word processor and graphic presentation tool. Microsoft Word and PowerPoint would be appropriate, or similar programs that can convert files to the RTF or PDF format. In addition, you may require certain Internet plug-ins for using articles, simulations, or videos inserted in some documents of this course. These are:
1. Adobe Reader
3. Macromedia Shockwave Player
Click to download and install these plug-ins.
Additional Resources
Each module of the course contains many links to Internet resources that are relevant to the specific content. In addition, students can benefit from the HCCC Library .
If you have a question about the readings and materials for this course, please post a question in the ” Ask a Question” area located at the bottom of the “Course Information” section of this course. Please be sure to give your post a meaningful subject and to check that area frequently for replies and new posts.
Contributors and Attributions
- Course Readings & Materials. Authored by : Kelly, Jessica. Provided by : Herkimer College. Project : ATD Course. License : CC BY: Attribution


8.2: Overview
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When Javier Lopez-Calderon and I designed the artifact rejection process in ERPLAB, Javier suggested that we should refer to the process of flagging epochs as artifact detection , because those epochs aren’t actually deleted from the EEG dataset. The rejection (or exclusion) of the flagged epochs actually occurs during the averaging process. I thought that was a great idea. So, I will use the phrase artifact detection to refer to the process of determining which epochs should be flagged and the phrase artifact rejection to refer to the process excluding flagged epochs from the averaged ERPs.
EEGLAB and ERPLAB also contain a separate set of routines that actually delete problematic segments of data from the continuous EEG. These routines are primarily used as a preprocessing step in the artifact correction process, as will be described in the next chapter. In the present chapter, the term artifact rejection will be used in the context of epoched EEG data.
Chapter 6 in Luck (2014) provides important theoretical background about a broad range of artifacts and about the nature of the artifact detection/rejection process. It will be helpful (but not absolutely necessary) for you to read that chapter before proceeding. The goal of the present chapter is to make this theoretical background more concrete and demonstrate the practical issues that arise in real data.
We’ll focus on data from a few example participants who I selected not because they had “good” data but because they were quite challenging. The data will come from two of the ERP CORE experiments (Kappenman et al., 2021), one looking at the mismatch negativity (MMN) and one looking at the N2pc component. The MMN paradigm was described in the previous chapter, and the N2pc paradigm will be described later in the present chapter. We’ll mainly consider blinks and eye movements, because they’re the most common large artifacts, but the exercises will also teach you general principles that you can use for other kinds of artifacts and other types of experiments.
Artifact correction has many advantages over artifact rejection, and it will be covered in the next chapter. In almost all cases, however, I recommend combining rejection and correction. Also, the problems created by artifacts are the same whether you’re using rejection or correction, so you’ll need to read at least the first part of this chapter even if you’re mainly planning to use correction instead of rejection.
Organization of the Chapter
Artifact detection is conceptually simple, but it requires a lot of decisions, and you need to know how to make the best decisions to achieve the best possible data. As a result, this chapter is pretty long. Here’s the overall structure:
- The first part of the chapter describes three main problems that are typically addressed by artifact rejection and provides an overview of the detection+rejection process.
- The second part of the chapter takes you through a series of exercises in which you’ll see how to detect and reject blinks, eye movements, and other miscellaneous artifacts in the context of the MMN experiment.
- The last part of the chapter takes you through exercises that teach you how to detect and reject small but consistent eye movements, which are especially problematic in experiments with lateralized target stimuli (especially N2pc and CDA experiments) or lateralized responses (mainly LRP experiments). If you don’t conduct experiments of this sort, you can skip this part of the chapter.
The exercises focus on data from only two participants in each experiment. I strongly recommend looking at the data from additional participants and repeating the artifact detection procedures with those participants. You can find the data from additional participants in the MMN_Data N2pc_Data folders inside the Chapter_8 folder.
Keep in mind that we did nothing to try to minimize blinking when designing and running these experiments because we knew we would use artifact correction rather than artifact rejection to deal with blinks. As a result, many participants blinked on a large proportion of trials. We would have needed to exclude many of these participants if we had rejected rather than corrected blinks.


14.10: Sample problems and solutions
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Exercise \(\PageIndex{1}\)
A clarinet can be modeled as an air column that is open at one end and closed at the other end, as in Figure \(\PageIndex{1}\).
- Draw the first three harmonics for a clarinet (draw the maximum displacement of the air molecules as a function of distance in the clarinet).
- Find an expression for the wavelength of the \(n^{th}\) harmonic for a clarinet of length \(L\) .
- If a clarinet is \(60\text{cm}\) long , what is the lowest frequency note it can produce?
- Answer
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a. The first three harmonics are are shown in Figure \(\PageIndex{2}\).
b. The equation for a standing wave is:
\[\begin{aligned} D(x,t)=2A\sin(kx)cos(\omega t)\end{aligned}\]
We let the fixed end be at \(x=0\) . At the fixed end, the displacement is equal to zero. At the free end ( \(x=L\) ) the displacement is maximized. The first condition is always true. The second condition will be met when:
\[\begin{aligned} \sin(kL)&=1\\[4pt] \therefore kL&=\pi/2,3\pi/2,...\\[4pt]\end{aligned}\]
This condition can be expressed as:
\[\begin{aligned} kL&=\frac{(2n-1)\pi}{2}\\[4pt] \frac{2\pi L}{\lambda}&=\frac{(2n-1)\pi}{2}\\[4pt] \therefore \lambda&=\frac{4L}{2n-1}\end{aligned}\]
where, in the second line, we used \(k=2\pi /\lambda\) . We can check that this formula works for the first three harmonics:
\[\begin{aligned} n=1: \quad \lambda&=\frac{4L}{2(1)-1} \\[4pt] L&=\frac{1}{4}\lambda \\[4pt] n=2: \quad \lambda&=\frac{4L}{2(2)-1} \\[4pt] L&= \frac{3}{4}\lambda \\[4pt] n=3: \quad \lambda&=\frac{4L}{2(3)-1} \\[4pt] L&= \frac{5}{4}\lambda \end{aligned}\]
Referring back to our diagram (Figure \(\PageIndex{2}\)), we can see that our formula holds true for the first three harmonics (i.e. for the first harmonic, the length of the clarinet is equal to \(1/4\) of a wavelength, etc.)
c. We found that the wavelength for the \(n^{th}\) wavelength is given by:
\[\begin{aligned} \lambda=\frac{4L}{2n-1}\end{aligned}\]
Writing \(\lambda\) in terms of the velocity, \(v\) , and frequency, \(f\) , gives:
\[\begin{aligned} \frac{v}{f}&=\frac{4L}{2n-1}\\[4pt] \therefore f&=\frac{v(2n-1)}{4L}\end{aligned}\]
From this formula, we can see that, if we want to find the lowest frequency, we want \(n=1\) . The length of the clarinet is \(0.6\text{m}\) , and \(v\) is the speed of sound in air which is \(343\text{m/s}\) at room temperature. Using these values, the lowest frequency is:
\[\begin{aligned} f&=\frac{(343\text{m/s})(2(1)-1)}{4(0.6\text{m})}\\[4pt] f&=143\text{Hz}\end{aligned}\]
Discussion: This frequency is close to the \(D_3\) note, which has a frequency of \(144\text{Hz}\) , so this answer makes sense. However, the value we found differs from the true value. Why might this be?
Exercise \(\PageIndex{2}\)
A pulse propagates down a rope of mass per unit length \(\mu_1\) that is tied to a second rope with a mass per unit length \(\mu_2\) (Figure \(\PageIndex{3}\)). The tensions in the ropes are equal in magnitude.
- Write the displacements of the incident pulse, the reflected pulse, and the transmitted pulse in the form \(D(x,t)=D(a(t\pm x/v))\) , where \(a\) is some constant that you need to determine, and the choice of \(+\) or \(-\) depends on the direction that the pulse is traveling in.
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The reflection coefficient,
\(R\)
, is the ratio of the amplitude of the reflected pulse to the amplitude of the incident pulse. Using the boundary conditions, show that the reflection coefficient is given by:
\[\begin{aligned} R=\frac{\sqrt{\mu_1}-\sqrt{\mu_2}}{\sqrt{\mu_1}+\sqrt{\mu_2}}\end{aligned}\]
Note: The boundary is the interface between the two ropes. By “using the boundary conditions”, we mean that you should think about what must be true at the boundary for this problem to make sense. Boundary conditions are often more obvious than you think!
- Answer
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a. We let the incident pulse move in the positive \(x\) direction (Figure \(\PageIndex{4}\)), and set \(x=0\) to be where the ropes connect.
The incident pulse (denoted by \(i\) ) is a traveling wave, moving in one dimension in the positive \(x\) direction. The incident pulse can thus be described by the function:
\[\begin{aligned} D_I(x,t)=A_I\cos(k_1x-\omega t)\\[4pt]\end{aligned}\]
We will use the formulas \(k=2\pi/\lambda\) and \(\omega=2\pi f\) to rewrite this equation in the form \(D=(a(t\pm x/v))\) . The frequency, \(f\) , of the wave will be the same in both ropes. The velocity of the wave, and therefore its wavelength, depends on the mass density of the rope. Since the incident wave travels through the first rope ( \(\mu_1\) ), its velocity will be \(v_1\) and its wavelength will be \(\lambda_1\) . The incident wave can thus be described by:
\[\begin{aligned} D_I&=A_I\cos\left( \frac{2\pi}{\lambda_1}x-2\pi ft\right)\\[4pt] &=A_I\cos \left( 2\pi\left(\frac{1}{\lambda_1}x- ft\right)\right)\\[4pt] &=A_I\cos \left( 2\pi f\left(\frac{x}{v_1}- t\right)\right)\\[4pt] &=A_I\cos \left( -2\pi f\left(t-\frac{x}{v_1}\right)\right)\\[4pt] D_I&=A_I\cos \left(2\pi f\left(t-\frac{x}{v_1}\right)\right)\end{aligned}\]
where we used \(v=f\lambda\) , and noted that \(\cos(-x)=\cos(x)\) .
The transmitted wave (denoted by the subscript \(T\) ) will also travel in the positive \(x\) direction, but its speed will be \(v_2\) , since it travels through the second rope:\[\begin{aligned} D_T&=A_T\cos \left( 2\pi f\left(t-\frac{x}{v_2}\right)\right)\end{aligned}\]
The reflected wave (denoted by \(R\) ) will travel in the \(-x\) direction and at the same speed as the incident pulse.
\[\begin{aligned} D_R&=A_R\cos \left( 2\pi f\left(t+\frac{x}{v_1}\right)\right)\end{aligned}\]
b. We will consider the boundary conditions at the interface between the two ropes. One boundary condition is that the rope must be continuous. As a result, the vertical displacement on the \(-x\) side of the boundary must be the same as the vertical displacement on the \(+x\) side of the boundary at every instant:
\[\begin{aligned} D_{-x}&=D_{+x}\quad\text{at $x=0$}\end{aligned}\]
The amplitude on the \(+x\) side is equal to the amplitude of the transmitted pulse. For the \(-x\) side of the boundary, we have to take into account that the incident and reflected pulses will superimpose (when the front of the incident pulse reaches the boundary, it will be reflected and interfere with the end of the incident pulse). This boundary condition can thus be expressed as:
\[\begin{aligned} A_I+A_R&=A_T\end{aligned}\]
The slope of the rope must also be continuous at the boundary. Since the incident and reflected pulses superimpose, and the principle of superposition states that the net displacement is the sum of the displacement of these two waves, we can write:
\[\begin{aligned} \frac{\partial}{\partial x}(D_I+D_R)\Bigr|_{x=0}&=\frac{\partial}{\partial x}D_T\Bigr|_{x=0}\\[4pt] \frac{\partial}{\partial x}D_I\Bigr|_{x=0}+\frac{\partial}{\partial x}D_R\Bigr|_{x=0}&=\frac{\partial}{\partial x}D_T\Bigr|_{x=0}\end{aligned}\]
Using our equations for the incident, transmitted, and reflected pulses found in part a), and taking the appropriate partial derivatives, this equation becomes:
\[\begin{aligned} (A_I/v_1) \sin \left(2\pi f\left( t-\frac{x}{v_1}\right)\right)\Bigr|_{x=0}+(-A_R/v_1) \sin \left( 2\pi f\left( t+\frac{x}{v_1}\right)\right)\Bigr|_{x=0}&=\\[4pt](A_T/v_2) \sin \left( 2\pi f\left( t-\frac{x}{v_2}\right)\right)\Bigr|_{x=0}\end{aligned}\]
Evaluating at \(x=0\) gives:
\[\begin{aligned} (A_I/v_1) \sin (2\pi ft) +(-A_R/v_1) \sin (2\pi ft)&=(A_T/v_2) \sin (2\pi ft)\\[4pt] \frac{A_I}{v_1} -\frac{A_R}{v_1}&=\frac{A_T}{v_2} \end{aligned}\]
Using our first condition, \(A_I+A_R=A_T\) , we get:
\[\begin{aligned} \frac{A_I}{v_1} -\frac{A_R}{v_1}&=\frac{A_I}{v_2}+\frac{A_R}{v_2}\\[4pt]\end{aligned}\]
Now, we can rearrange to find the reflection coefficient, \(R=A_R/A_I\) :
\[\begin{aligned} A_I\left( \frac{v_2-v_1}{v_1v_2}\right)&=A_R\left( \frac{v_2+v_1}{v_1v_2}\right)\\[4pt] R&=\frac{v_2-v_1}{v_2+v_1}\end{aligned}\]
Since the velocities in the first and second rope are \(v_1=\sqrt{F_T/\mu_1}\) and \(v_2=\sqrt{F_T/\mu_2}\) , respectively, the reflection coefficient can be written as:
\[\begin{aligned} R&=\frac{\sqrt{\frac{F_T}{\mu_2}}-\sqrt{\frac{F_T}{\mu_1}}}{\sqrt{\frac{F_T}{\mu_2}}+\sqrt{\frac{F_T}{\mu_1}}}\\[4pt] &=\frac{\sqrt{F_T}}{\sqrt{F_T}}\cdot \frac{\frac{1}{\sqrt{\mu_2}}-\frac{1}{\sqrt{\mu_1}}}{\frac{1}{\sqrt{\mu_2}}+\frac{1}{\sqrt{\mu_1}}}\\[4pt] \therefore R&=\frac{\sqrt{\mu_1}-\sqrt{\mu_2}}{\sqrt{\mu_1}+\sqrt{\mu_2}}\end{aligned}\]
as desired.


2: Equations and Inequalities
Source: Boundless. “Equations and Inequalities.” Boundless Algebra . Boundless, 21 Jul. 2015. Retrieved 22 Dec. 2015 from www.boundless.com/algebra/te...ties-63-10904/
Source: Boundless. “Equations and Inequalities.” Boundless Algebra . Boundless, 21 Jul. 2015. Retrieved 22 Dec. 2015 from www.boundless.com/algebra/te...ties-63-10904/
An equation states that two expressions are equal, while an inequality relates two different values.
Source: Boundless. “Equations and Inequalities.” Boundless Algebra. Boundless, 21 Jul. 2015. Retrieved 22 Dec. 2015 from www.boundless.com/algebra/te...ties-63-10904/
Source: Boundless. “Equations and Inequalities.” Boundless Algebra. Boundless, 21 Jul. 2015. Retrieved 22 Dec. 2015 from www.boundless.com/algebra/te...ties-63-10904/
Recall that a function is a relation that assigns to every element in the domain exactly one element in the range. Linear functions are a specific type of function that can be used to model many real-world applications, such as plant growth over time. In this chapter, we will explore linear functions, their graphs, and how to relate them to data.
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- 2.1: The Rectangular Coordinate Systems and Graphs
- Descartes introduced the components that comprise the Cartesian coordinate system, a grid system having perpendicular axes. Descartes named the horizontal axis the \(x\)-axis and the vertical axis the \(y\)-axis. This system, also called the rectangular coordinate system, is based on a two-dimensional plane consisting of the \(x\)-axis and the \(y\)-axis. Perpendicular to each other, the axes divide the plane into four sections. Each section is called a quadrant.
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- 2.3: Models and Applications
- A linear equation can be used to solve for an unknown in a number problem. Applications can be written as mathematical problems by identifying known quantities and assigning a variable to unknown quantities. There are many known formulas that can be used to solve applications. Distance problems are solved using the \(d = rt\) formula. Many geometry problems are solved using the perimeter formula \(P =2L+2W\), the area formula \(A =LW\), or the volume formula \(V =LWH\).
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- 2.4: Complex Numbers
- The square root of any negative number can be written as a multiple of i. To plot a complex number, we use two number lines, crossed to form the complex plane. The horizontal axis is the real axis, and the vertical axis is the imaginary axis. Complex numbers can be added and subtracted by combining the real parts and combining the imaginary parts. Complex numbers can be multiplied and divided.
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- 2.5: Quadratic Equations
- Many quadratic equations can be solved by factoring when the equation has a leading coefficient of 1 or if the equation is a difference of squares. The zero-factor property is then used to find solutions. Many quadratic equations with a leading coefficient other than 1 can be solved by factoring using the grouping method. Another method for solving quadratics is the square root property. The variable is squared. We isolate the squared term and take the square root of both sides of the equation.
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- 2.6: Other Types of Equations
- Rational exponents can be rewritten several ways depending on what is most convenient for the problem. To solve, both sides of the equation are raised to a power that will render the exponent on the variable equal to 1. Factoring extends to higher-order polynomials when it involves factoring out the GCF or factoring by grouping. We can solve radical equations by isolating the radical and raising both sides of the equation to a power that matches the index.
Contributors and Attributions
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Jay Abramson (Arizona State University) with contributing authors. Textbook content produced by OpenStax College is licensed under a Creative Commons Attribution License 4.0 license. Download for free at https://openstax.org/details/books/precalculus .


15.11: Ribosomes and Protein Synthesis - The Mechanism of Protein Synthesis
- Describe the process of translation
As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination.
Initiation of Translation
Protein synthesis begins with the formation of a pre-initiation complex. In E. coli , this complex involves the small 30S ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special initiator tRNA, called fMet-tRNA. The initiator tRNA basepairs to the start codon AUG (or rarely, GUG) and is covalently linked to a formylated methionine called fMet. Methionine is one of the 21 amino acids used in protein synthesis; formylated methionine is a methione to which a formyl group (a one-carbon aldehyde) has been covalently attached at the amino nitrogen. Formylated methionine is inserted by fMet-tRNA at the beginning of every polypeptide chain synthesized by E. coli , and is usually clipped off after translation is complete. When an in-frame AUG is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNA. In E. coli mRNA, a sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template.
In eukaryotes, a pre-initiation complex forms when an initiation factor called eIF2 ( eukaryotic initiation factor 2) binds GTP, and the GTP-eIF2 recruits the eukaryotic initiator tRNA to the 40s small ribosomal subunit. The initiator tRNA, called Met-tRNA i , carries unmodified methionine in eukaryotes, not fMet, but it is distinct from other cellular Met-tRNAs in that it can bind eIFs and it can bind at the ribosome P site. The eukaryotic pre-initiation complex then recognizes the 7-methylguanosine cap at the 5′ end of a mRNA. Several other eIFs, specifically eIF1, eIF3, and eIF4, act as cap-binding proteins and assist the recruitment of the pre-initiation complex to the 5′ cap. Poly (A)-Binding Protein (PAB) binds both the poly (A) tail of the mRNA and the complex of proteins at the cap and also assists in the process. Once at the cap, the pre-initiation complex tracks along the mRNA in the 5′ to 3′ direction, searching for the AUG start codon. Many, but not all, eukaryotic mRNAs are translated from the first AUG sequence. The nucleotides around the AUG indicate whether it is the correct start codon.
Once the appropriate AUG is identified, eIF2 hydrolyzes GTP to GDP and powers the delivery of the tRNA i -Met to the start codon, where the tRNA i anticodon basepairs to the AUG codon. After this, eIF2-GDP is released from the complex, and eIF5-GTP binds. The 60S ribosomal subunit is recruited to the pre-initiation complex by eIF5-GTP, which hydrolyzes its GTP to GDP to power the assembly of the full ribosome at the translation start site with the Met-tRNAi positioned in the ribosome P site. The remaining eIFs dissociate from the ribosome and translation is ready to begins.
In archaea, translation initiation is similar to that seen in eukaryotes, except that the initiation factors involved are called aIFs (archaeal inititiaion factors), not eIFs.
Translation Elongation
The basics of elongation are the same in prokaryotes and eukaryotes. The intact ribosome has three compartments: the A site binds incoming aminoacyl tRNAs; the P site binds tRNAs carrying the growing polypeptide chain; the E site releases dissociated tRNAs so that they can be recharged with amino acids. The initiator tRNA, rMet-tRNA in E. coli and Met-tRNA i in eukaryotes and archaea, binds directly to the P site. This creates an initiation complex with a free A site ready to accept the aminoacyl-tRNA corresponding to the first codon after the AUG.
The aminoacyl-tRNA with an anticodon complementary to the A site codon lands in the A site. A peptide bond is formed between the amino group of the A site amino acid and the carboxyl group of the most-recently attached amino acid in the growing polypeptide chain attached to the P-site tRNA.The formation of the peptide bond is catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the large ribosomal subunit. The energy for the peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor.
Catalyzing the formation of a peptide bond removes the bond holding the growing polypeptide chain to the P-site tRNA. The growing polypeptide chain is transferred to the amino end of the incoming amino acid, and the A-site tRNA temporarily holds the growing polypeptide chain, while the P-site tRNA is now empty or uncharged.
The ribosome moves three nucleotides down the mRNA. The tRNAs are basepaired to a codon on the mRNA, so as the ribosome moves over the mRNA, the tRNAs stay in place while the ribosome moves and each tRNA is moved into the next tRNA binding site. The E site moves over the former P-site tRNA, now empty or uncharged, the P site moves over the former A-site tRNA, now carrying the growing polypeptide chain, and the A site moves over a new codon. In the E site, the uncharged tRNA detaches from its anticodon and is expelled. A new aminoacyl-tRNA with an anticodon complementary to the new A-site codon enters the ribosome at the A site and the elongation process repeats itself. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP.
Translation termination
Termination of translation occurs when the ribosome moves over a stop codon (UAA, UAG, or UGA). There are no tRNAs with anticodons complementary to stop codons, so no tRNAs enter the A site. Instead, in both prokaryotes and eukaryotes, a protein called a release factor enters the A site. The release factors cause the ribosome peptidyl transferase to add a water molecule to the carboxyl end of the most recently added amino acid in the growing polypeptide chain attached to the P-site tRNA. This causes the polypeptide chain to detach from its tRNA, and the newly-made polypeptide is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.
Modeling translation : This interactive models the process of translation in eukaryotes.
Key Points
- Protein synthesis, or translation, begins with a process known as pre-initiation, when the small ribosmal subunit, the mRNA template, initiator factors, and a special initiator tRNA, come together.
- During translocation and elongation, the ribosome moves one codon 3′ down the mRNA, brings in a charged tRNA to the A site, transfers the growing polypeptide chain from the P-site tRNA to the carboxyl group of the A-site amino acid, and ejects the uncharged tRNA at the E site.
- When a stop or nonsense codon (UAA, UAG, or UGA) is reached on the mRNA, the ribosome terminates translation.
Key Terms
- translation : a process occurring in the ribosome in which a strand of messenger RNA (mRNA) guides assembly of a sequence of amino acids to make a protein


Studying is hard work, but you can still learn some techniques to help you be a more effective learner. Two major and interrelated techniques involve avoiding distractions to the best of your ability and creating a study environment that works to help you concentrate.
IN the classroom
Attend Every Class
Attending each and every class requires a lot of self-discipline and motivation. Doing so will help you remain engaged and involved in course topics, provide insight into what your instructor deems most important, allow you to submit work and receive your graded assignments, and give you the opportunity to take quizzes or exams that cannot be made up.
Missing class is a major factor in students dropping courses or receiving poor grades. In addition, students attempting to make up the work from missing class often find it overwhelming. It’s challenging to catch up if we get behind.
Sit Front and Center
Even if your faculty says, “Sit wherever you want — sit where you are most comfortable,” think about where you would want to be if you were to attend a concert for your favorite artist. The answer is most often in front of the stage, because the best experience is closest to the band. That’s why front-and-center tickets are the most expensive. There are some reasons sitting in the back works for some students, but you run the risk of sitting behind someone you cannot see over. And if you’re sitting in the back so that you can send text messages without being seen, work on something else or so that you can disengage (not pay attention without the instructor noticing), then you’re sitting in the back for the wrong reasons. Rather than hiding, you want to create the best learning environment, from both a visual and auditory perspective.
Ask Questions
Many students feel like they are the only one that has a question or the only one that doesn’t understand something in class. Ask questions during class, especially if your instructor encourages them. If not, make the effort to ask your questions before or after class or during your instructors’ office hours.
If you take a class offered online, ask a lot of questions via the preferred method your instructor recommends. Since the delivery method is different to what most students are used to, students in online courses tend to have more questions. Online students may ask questions to understand the material and to be able to successfully navigate through the course content.
Outside of the classroom
Be Prepared for Each Class
Complete your assigned reading ahead of the deadline. Follow the syllabus so that you’ll have familiarity with what the instructor is speaking about. Bring your course syllabus, textbook, notebook and any handouts or other important information for each particular class along with a pen and a positive attitude. Become interested in what the instructor has to say. Be eager to learn. Sleep adequately the night before class and ensure you do not arrive to class on an empty stomach. Many courses, both in person and online, use digital platforms called Learning Management Systems (LMS). Examples of these are Canvas, Blackboard, and Moodle. It is important for students to check their e-mail regularly as well as announcements or notifications from their instructor through the LMS.
Read and Retain Your Syllabus
In addition to acting as a contract between the instructor and you, the syllabus is also often the source of information for faculty contact information, textbook information, classroom behavior expectations, and attendance policy and course objectives. Some students make the mistake of stuffing the syllabus in their backpack when they receive it on the first day of class and never take a look at it again. Those who clearly read it, keep it for reference and review it frequently find themselves more prepared for class. If there is something in the syllabus you don’t understand, ask your instructor about it before class, after class or during their office hours.
 Successful students will also schedule when to start those assignments and have an idea of how long it will take to complete them.
It’s easy to put off studying if it’s not something we schedule. Block specific times and days for studying. Put the times on your calendar. Stick to the schedule.
Complete All of Your Assigned Readings & Assignments (On Time)
There will be things that you are more interested in doing than your assignments and unexpected life happenings that will come up. Students who earn good grades have the motivation and discipline to complete all of their assignments.
College courses have a significant amount of assigned reading and it can take a while to become comfortable with the workload. Some students fall behind early in keeping up with the reading requirements and others fail to read it at all. You will be most prepared for your class and for learning if you complete the reading assigned before your class. Staying on top of your syllabus and class calendar will help you be aware of your reading assignment deadlines. (See
Chapter 3.2
for more help with pre-reading).
 Find out what is available to you by checking your school’s website for campus resources or student services, or talk to an academic advisor or counselor about what resources may be helpful for you.
Review for Exams
Preparation for an exam should begin on the first day of class, not when the exam is announced nor the night before an exam. Review your notes frequently to keep material fresh in your head.
Have Someone Read Your Papers Before You Submit Them
You might be surprised to learn how many students turn in papers with spelling, grammar and punctuation errors that could have been easily corrected by using a spellchecker program or having someone read your paper. Many schools offer writing centers or tutors who will read your paper and give feedback, make suggestions, and help shape ideas. Take advantage of these services if they are offered. Another strategy is to read your paper aloud to yourself. You may catch errors when you read aloud that you might not catch when reading your writing. Remember that it is always the students’ responsibility to have papers proofread, not someone else’s.
Your Study Space
Study At a Time and Location That Is Best for You
Some students study best in the morning and some at night. Some excel at a coffee shop, and others at the library. The place and time in which students often study is usually the most convenient for them. Students often find convenient places and times may also be full of distractions and thus are not good choices for them to study. It’s worth the effort to study at the time and place that will be most productive for you. For most students, it is best to turn off the cell phone and TV and to keep off the Internet (and social media) unless it directly relates to your work.
Tips for Effective, Individual Study Spaces
Most students take what they can get when it comes to study areas. Schools usually offer a variety of nooks and crannies for students to hunker down and get their assignments done. The school library is a good (and quiet) place. Many common areas elsewhere on campus have tables, chairs, couches, and lounges to accommodate learners. But most students end up doing the majority of their out-of-class work at home.
Home environments may be limited in terms of providing all of the recommended aspects of a good study space, but many of the recommendations can be either implemented or adapted from what a student has on hand or what can be improvised no matter what environment they are living in. Elements conducive to a more effective study/homework experience include such things as good lighting, ample supplies, comfortable seating, adequate space, and personalizing the study area to add a touch of inspiration and motivation.
Avoiding Distractions
We have always had distractions—video games, television shows, movies, music, friends—even housecleaning can distract us from doing something else we need to do, like study for an exam. That may seem extreme, but sometimes vacuuming is the preferred activity to buckling down and working through calculus problems! Cell phones, tablets, and portable computers that literally bring a world of possibilities to us anywhere have brought
distraction
to an entirely new level. When was the last time you were with a large group of people when you didn’t see at least a few people on devices?
Figure 7.2: Video games are a common distraction, but we need to be aware that even tedious activities like cleaning can be a distraction from studying.
When you study, your biggest challenge may be to block out all the competing noise. And letting go of that connection to our friends and the larger world, even for a short amount of time, can be difficult. Perhaps the least stressful way to allow yourself a distraction-free environment is to make the study session a definite amount of time: long enough to get a significant amount of studying accomplished but short enough to hold your attention.
You can increase that attention time with practice and focus. Pretend it is a professional appointment or meeting during which you cannot check e-mail or texts or otherwise engage with your portable devices. We have all become very attached to the ability to check in—anonymously on social media or with family and friends via text, chat, and calls. If you set a specific amount of time to study without interruptions, you can convince your wandering mind that you will soon be able to return to your link to the outside world. Start small and set an alarm—a 30-minute period to review notes, then a brief break, then another 45-minute study session to quiz yourself on the material, and so on.
When you prepare for your optimal study session, remember to do these things:
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Put your phone out of sight—in another room or at least some place where you will not see or hear it vibrate or ring. Just flipping it over is not enough.
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Turn off the television or music (more on that in the next section).
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Unless you are deliberately working with a study group, study somewhere alone if possible or at least away from others enough to not hear them talking.
If you live with lots of other people or don’t have access to much privacy, see if you can negotiate some space alone to study. Ask others to leave one part of the house or an area in one room as a quiet zone during certain hours. Ask politely for a specific block of time; most people will respect your educational goals and be willing to accommodate you. If you’re trying to work out quiet zones with small children in the house, the bathtub with a pillow can make a fine study oasis.
Study Environment
You may not always be in the mood or inspired to study. And if you have a long deadline, maybe you can blow off a study session on occasion, but you shouldn’t get into the habit of ignoring a strong study routine. Jane Austen once wrote in a letter, “I am not at all in a humor for writing; I must write on till I am.” Sometimes just starting is the hard part; go ahead and begin. Don’t wait around for your study muse; start working, and she’ll show up.
Sometimes you just need to plop down and study whenever and wherever you can manage—in the car waiting for someone, on the bus, at the Little League field as you cheer on your shortstop. And that’s OK if this is the exception. For long-term success in studying, though, you need a better study setting that will help you get the most out of your limited study time. Whatever your space limitations, carve out a place that you can dedicate to reading, writing, note taking, and reviewing. This doesn’t need to be elaborate and expensive—all you truly need is a flat surface large enough to hold either your computer or writing paper, book or notes, pens/pencils/markers, and subject-specific materials you may need (e.g., stand-alone calculators, drawing tools, and notepads).  What do you have now that you consider your study space? Is it set up for your optimal success?
Figure 7.3: Which is before, and which is after? (Credit: Ali West / Flickr / Attribution 2.0 Generic (CC-BY 2.0))
If it is at all possible, try to make this area exclusive to your study sessions and something you can leave set up all the time and a place out of the way of family or roommate traffic. For example, Martina thought setting up her study station on the dining room table was a good idea at first. The view was calming, and the table was big enough to spread out and could even hold all her materials to study architectural drawings, her favorite subject. But then she needed the table for a small family dinner party, so she had to find a cubbyhole to hide away her supplies with some needing to go into a closet in the next room. Now she was spread out over multiple study spaces. And the family TV was in an adjacent room, not visible from the table but certainly an auditory distraction. Martina ultimately decided to forgo her view and create a smaller station in an unused bedroom so she could leave her supplies out and have a quieter area. You may have to try out numerous places to determine what works best for you.
 You should include the basics: a good chair, a work surface, and whatever materials, books, notes, and other supplies you need for the subject you are studying. If you want to make it even more of a productive place, you can look in magazines for ideas or search the web to see how others have set up simple areas or more elaborate arrangements.
You don’t need an elaborate setting, but you may want to consider including a few effective additions if you have the space:
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small bulletin board for often-used formulas
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encouraging quotes or pictures of your goal
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whiteboard for brainstorming
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sticky notes for reminders in texts and notes
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file holder for most-used documents
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bookshelf for reference books
Activity
Describe every element in your ideal study environment and explain why it’s there as well as how it will make more efficient use of your time, limit distractions, or in some other way strengthen your ability to study.
After you have described your ideal study environment, think about how you can adapt that environment if you cannot be in your favorite place to study. How do you
make your own space
in the library, a student lounge, or a dedicated space on campus for student studying?
Debunking Study Myths
MYTH #1: You can multitask while studying.
How many times do you eat in the car? Watch TV while you write out a grocery list? Listen to music while you cook dinner? What about type an e-mail while you’re on the phone with someone else and jot down notes about the call? The common term for this attempt to do more than one thing at a time is multitasking, and almost everyone does it at some point. On some days, you simply cannot accomplish all that you want to get done, so you double up. The problem is, multitasking doesn’t really work. Of course, it exists, and we do it. For instance, we walk and chew gum or drive and talk, but we are not really thinking about two or more distinct things or doing multiple processes simultaneously.
MYTH #2: Highlighting main points of a text is useful.
Another myth of studying that seems to have a firm hold is that the idea of highlighting text—in and of itself—is the best way to review study material. It is one way, and you can get some benefit from it, but don’t trick yourself into spending too much time on this surface activity and consider your study session complete. Annotating texts or notes is a first-step type of study practice. If you allow it to take up all your time, you may want to think you are fully prepared for an exam because you put in the time. Actually, you need much more time reviewing and retrieving your lessons and ideas from the text or class lecture as well as quizzing yourself to accomplish your goal of learning so you can perform well on the exam. Highlighting is a task you can do rather easily, and it makes you feel good because you are actively engaging with your text, but true learning needs more steps.
MYTH #3: Studying effectively is effortless.
There is nothing effortless, or even pleasant at times, about studying. This is why so many students don’t put in the time necessary to learn complex material: it takes time, effort, and, in some cases, a little drudgery. This is not to say that the outcome, learning—and maybe making an A—is not pleasant and rewarding. It is just that when done right, learning takes focus, deliberate strategies, and time. Think about a superstar athlete who puts in countless hours of drills and conditioning so that she makes her work on the field look easy. If you can also
enjoy
the studying, the skill development, and the knowledge building, then you will most likely be more motivated to do the work.
Analysis Question
When are you most liable to multitask? How could you be more aware of this practice and try to eliminate it, especially when it comes to studying? How can you make your initial text highlighting more time efficient so you can include other study practices?
Study Strategies
Everyone wishes they had a better memory or a stronger way to use memorization. You can make the most of the memory you have by making some conscious decisions about how you study and prepare for exams. Incorporate these ideas into your study sessions:
Practicing effective memorization is when you use a trick, technique, or strategy to recall something—for another class, an exam, or even to bring up an acquaintance’s name in a social situation. Really whatever works for you to recall information is a good tool to have. You can create your own quizzes and tests to go over material from class. You can use mnemonics to jog your memory. You can work in groups to develop unique ways to remember complex information. Whatever methods you choose to enhance your memory, keep in mind that repetition is one of the most effective tools in any memory strategy. Do whatever you do over and over for the best results.
Using Mnemonics
Mnemonics (pronounced new-monics) are a way to remember things using reminders. Did you learn the points of the compass by remembering NEWS (north, east, west, and south)? Or the notes on the music staff as FACE or EGBDF (every good boy does fine)? These are mnemonics. When you’re first learning something and you aren’t familiar with the foundational concepts, these help you bring up the information quickly, especially for multistep processes or lists. After you’ve worked in that discipline for a while, you likely don’t need the mnemonics, but you probably won’t forget them either.
Here are some familiar mnemonics you may find useful:
Figure 7.4
You can certainly make up your own mnemonics, but be careful that your reminder isn’t so complex and convoluted that it is more difficult to remember than the information you were relating it to!
Analysis Question
Do you have other mnemonics that help you remember difficult material? What are they? How have they helped you with remembering important things?
Practicing Concept Association
When you study, you’re going to make connections to other things—that’s a good thing. It shows a highly intelligent ability to make sense of the world when you can associate like and even somewhat unlike components. If, for instance, you were reading Martin Luther King Jr.’s “Letter from a Birmingham Jail,” and you read the line that he had been in Birmingham, you may remember a trip you took with your family last summer through Alabama and that you passed by and visited the civil rights museum in Birmingham. This may remind you of the different displays you saw and the discussions you had with your family about what had happened concerning civil rights in the 1950s,’60s, and ’70s in the United States.
This is a good connection to make, but if your assignment is to critique the literary aspects of King’s long epistle, you need to be able to come back to the actual words of the letter and see what trends you can see in his writing and why he may have used his actual words to convey the powerful message. The connection is fine, but you can’t get lost in going down rabbit holes that may or may not be what you’re supposed to be doing at the time. Make a folder for this assignment where you can put things such as a short summary of your trip to Alabama. You may eventually include notes from this summary in your analysis. You may include something from a website that shows you information about that time period. Additionally, you could include items about Martin Luther King Jr.’s life and death and his work for civil rights. All of these elements may help you understand the significance of this one letter, but you need to be cognizant of what you’re doing at the time and remember it is not usually a good idea to just try to keep it all in your head. The best idea is to have a way to access this information easily, either electronically or in hard copy, so that if you are able to use it, you can find it easily and quickly.
 For example, Andrea is an avid knitter and remembers how to create complicated stitches by associating them with nursery rhymes she read as a child. A delicate stitch that requires concentration because it makes the yarn look like part of it is hiding brings to mind Red Riding Hood, and connecting it to that character helps Andrea recall the exact order of steps necessary to execute the design. You can do the same thing with song lyrics, lines from movies, or favorite stories where you draw a connection to the well-known phrase or song and the task you need to complete.
Application
Choose one of the following, and create an idea cluster to group and organize:
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Example A: aviation jobs in North America
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Example B: the use of analytics in sports to determine team rosters
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Example C: how social media affects political campaigns
Start the idea cluster with the topic circled in the middle of the page. For Example A, you might make one cluster off the main circle for specific positions; you could add another cluster for salary ranges and another for geographic regions.
Three Effective Study Strategies
There are more than three study strategies, but focusing on the most effective strategies will make an enormous difference in how well you will be able to demonstrate learning (also known as “acing your tests”). Here is a brief overview of each of the three strategies:
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Spacing—This has to do with
when
you study. Hint: Don’t cram; study over a period of days, preferably with “breaks” in between.
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Interleaving—This has to do with
what
you study. Hint: Don’t study just one type of content, topic, chapter, or unit at a time; instead, mix up the content when you study.
-
Practice testing—This has to do with
how
you study. Hint: Don’t just reread content. You must quiz or test your ability to retrieve the information from your brain.
Spacing
We all know that cramming is not an effective study strategy, but do we know why? Research on memory suggests that giving yourself time in between study sessions actually helps you forget the information. And forgetting, which sounds like it would be something you
don’t
want to do, is actually good for your ability to remember information long-term. That’s because every time you forget something, you need to relearn it, leading to gains in your overall understanding and “storage” of the material. The table below demonstrates how spacing works. Assume you are going to spend about four hours studying for a Sociology exam. Cramming would have you spending most of those four hours the night before the exam. With spacing, on the other hand, you would study a little bit each day.
Table 7.1
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Spacing
|
|
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Sunday
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Monday
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Tuesday
|
Wednesday
|
Thursday
|
Friday
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Saturday
|
|
Cramming
|
|
|
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Study for 1 hour
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Study for 3
|
|
|
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Spacing
|
Study for 1 hour
|
|
Study for 30 minutes
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Study for 1 hour
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Study for 90 minutes
|
|
|
Interleaving
One particular studying technique is called interleaving, which calls for students to mix up the content that is being studied. This means not just spending the entire study session on one sort of problem and then moving on to a different sort of problem at a later time.
If you take the schedule we used for the spacing example above, we can add the interleaving concepts to it. Notice that interleaving includes revisiting material from a previous chapter or unit or revisiting different types of problems or question sets. The benefit is that your brain is “mixing up” the information, which can sometimes lead to short-term forgetting but can lead to long-term memory and learning.
Table 7.2
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Interleaving
|
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Sunday
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Monday
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Tuesday
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Wednesday
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Thursday
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Friday
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Reread Sociology, Chapter 1.
Reorganize notes
|
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Reread Sociology, Chapter 1 and 2
Take Ch 1 online quiz.
Create Chapter 2 concept map
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Reread Sociology, Chapters 1-3.
Take online quizzes for chapters 2 and 3.
Reorganize notes.
Create practice test
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Reread notes.
Review items missed on online quizzes.
Take practice test and review challenge areas.
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TEST in sociology, Chapters 1-3
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Practice Testing
You can do a practice “test” in two ways. One is to test yourself as you are reading or taking in information. This is a great way to add a little variety to your studying. You can ask yourself what a paragraph or text section means as you read. To do this, read a passage in a text, cover up the material, and ask yourself, “What was the main idea of this section?” Recite aloud or write down your answer, and then check it against the original information.
Another, more involved, way to practice test is to create flashcards or an actual test by writing a test. This takes more time, but there are online programs such as Quizlet that make it a little easier. Practice testing is an effective study strategy because it helps you practice
retrieving
information, which is what you want to be able to do when you are taking the real test.
One of the best ways to learn something is to teach it to someone else, so ask a friend or family member if you can explain something to them, and
teach
them the lesson. You may find you know more about the subject than you thought . . . or you may realize quickly that you need to do more studying. Why does teaching someone else rank as one of the most effective ways to learn something? It is a form of practice testing that requires you to demonstrate you know something in front of someone else!
Recognizing Strengths/Weaknesses of Preferred Study Approaches
Most children don’t learn to ride a bicycle by reading a manual; they learn by watching other kids, listening to instructions, and getting up on the seat and learning to balance—sometimes with training wheels or a proud parent holding on, but ultimately without any other support. They may fall over and feel insecure, but usually, they learn to make the machine go. Most of us employ multiple methods of study all the time. You usually only run into trouble if you stubbornly rely on just one way to learn or study and the material you’re studying or the task you want to accomplish doesn’t lend itself to that preference. You can practice specific strategies to help you learn in your preferred learning approach. Can you think of a time when the way you usually study a situation didn’t work?
When deciding on a study approach, consider what you know about the material and the type of knowledge it involves. Is it a group of concepts related to problem-solving methods, such as those you’d find in a physics class? Or is it a literary analysis of a novel? Consider as many elements as possible about the material -- and the way the material will be assessed -- to help choose a study approach.
You should also consider your instructor’s preferred method of teaching and learning. Watching the way they teach lessons or convey necessary course information to the class. Do they almost always augment lessons with video clips to provide examples or create a memorable narrative? Do they like to show you how something works by demonstrating and working with their hands—for instance, assembling a piece of equipment by taking it apart and putting it back together again? Echoing their teaching approach may help your study. That doesn’t mean you have to change your entire learning approach to match your instructors’ methods. Many instructors understand that their students will have different ways of learning and try to present information in multiple ways.
Practicing Active Continuous Improvement for All Preferences
You can certainly learn through specific approaches or according to specific preferences, but you will also need to adapt to different situations, skills, and subject areas. Don’t limit yourself to thinking you can
only
learn one way or another. That mindset induces anxiety when you encounter a learning situation that doesn’t match your preference. What if your instructor
only
uses a spoken lecture to teach concepts in your chemistry class, and you consider yourself a visual learner? Or what if the only method presented to you for learning mathematical computations is to see videos of others working problems, and you’re more hands-on? You may have to concentrate in a different way or devise other strategies to learn, but you can do it. In fact, you should sometimes work on the styles/preferences that you feel are your least favorite; it will actually strengthen your overall ability to learn and retain information.
10
Dr. Stephen Covey, famous leadership coach and businessman, called this attention to knowing and honing all your skill sets, not just your favorites,
sharpening the saw.
He advised that people should be aware of their strengths but should always hone their weaknesses by saying, “We must never become too busy sawing to take time to sharpen the saw.”
11
For instance, in the chemistry lecture example, you may need to take good notes from the spoken lecture and then review those notes as you sketch out any complex ideas or formulas. If the math videos are not enough for you to grasp difficult problems, you may ask for or find your own problems for additional practice covering that particular mathematical concept to solve on your own.
Effective studying is an ongoing process of reviewing course material. The first and most important thing you should know is that studying is not something you do a few days before an exam. To be effective, studying is something you do as part of an ongoing learning process, throughout the duration of the term.
Studying before the Exam
At least a week before a major exam, ask yourself these questions: What has the instructor said about what is included on the exam? Has the instructor said anything about what types of questions will be included? If you were the instructor, what questions would you ask on an exam? Challenge yourself to come up with some really tough open-ended questions. Think about how you might answer them. Be sure to go to any review sessions the instructor or your section leader holds.
Now go back and review your outlines. Do they cover what the instructor has suggested might be on the exam? After reviewing your outlines, reread the sections of your notes that are most closely associated with expected exam questions. Pay special attention to those items the instructor emphasized during class. Read key points aloud and write them down on index cards. Make flash cards to review in downtimes, such as when you’re waiting for a bus or for a class to start.
Studying in Groups
Figure 7.5
A study group that is too large is more likely to digress into casual conversation.
Study groups are a great idea—as long as they are thoughtfully managed. A study group can give you new perspectives on course material and help you fill in gaps in your notes. Discussing course content will sharpen your critical thinking related to the subject, and being part of a group to which you are accountable will help you study consistently. In a study group, you will end up “teaching” each other the material, which is the strongest way to retain new material. But remember, being in a group working together doesn’t mean there will be less work for you as an individual; your work will just be much more effective.
Here are some tips for creating and managing effective study groups:
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Think small.
Limit your study group to no more than three or four people. A larger group would limit each student’s participation and make scheduling of regular study sessions a real problem.
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Go for quality.
Look for students who are doing well in the course, who ask questions, and who participate in class discussions. Don’t make friendship the primary consideration for who should be in your group. Meet up with your friends instead during “social time”—study time is all about learning.
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Look for complementary skills and learning styles.
Complementary skills make for a good study group because your weaknesses will be countered by another student’s strengths. When a subject requires a combination of various skills, strengths in each of those skills is helpful (e.g., a group with one student who is really good at physics and another at math would be perfect for an engineering course). Finally, a variety of learning styles is helpful because each of you pick up differing signals and emphases from the instructor that you can share with each other, so you will not likely miss important points.
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Meet regularly.
When you first set up a study group, agree to a regular meeting schedule and stick to it. Moving study session times around can result in nonparticipation, lack of preparation, and eventually the collapse of the study group. Equally important is keeping your sessions to the allotted times.
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Define an agenda and objectives.
 Based on requests and comments from the group, the moderator should develop the agenda and start each session by summarizing what the group expects to cover and then keep the group to task.
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Include some of the following items on your agenda:
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Review and discuss class and assignment notes since your last meeting.
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Discuss assigned readings.
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Quiz each other on class material.
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“Reteach” aspects of the material team participants are unsure of.
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Brainstorm possible test questions and responses.
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Review quiz and test results and correct misunderstandings.
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Critique each other’s ideas for paper themes and approaches.
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Define questions to ask the instructor.
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Assign follow-up work.
If there is any work that needs to be done between meetings, make sure that all team members know specifically what is expected of them and agree to do the work.
-
Rotate the role of moderator or discussion leader.
This helps ensure “ownership” of the group is spread equally across all members and ensures active participation and careful preparation.


14: Appendix 3: Example Processing Pipeline
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- Last updated
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This appendix provides an example of a typical EEG preprocessing pipeline for a single participant, including all the steps prior to averaging. It is nearly identical to the pipeline scripts provided in the second half of the chapter on Scripting (Chapter 10). Much of the logic for the ordering of the steps is spelled out in Luck (2014), especially Appendix 1.
This pipeline is optimized for the kinds of experiments typically conducted in my lab, such as the ERP CORE experiments, in which highly cooperative college student participants are tested with in relatively simple cognitive tasks. Changes will often be necessary for different types of tasks and/or participants. In other words, don’t blindly follow this pipeline!
Step 1: Preprocessing Prior to ICA-Based Artifact Correction
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Import the participant’s original EEG data file(s) into EEGLAB
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If there are multiple data files (e.g., one per trial block), combine them into a single dataset.
- If the cap was removed and replaced between data files (e.g., because you had recording sessions on multiple days), you should merge the data files after the ICA step (because the electrodes might not be in exactly the same places for the different files, which will mess up ICA but isn’t a big deal for most other kinds of analyses).
- If a given channel is bad in a subset of the blocks, you could interpolate that channel for those blocks at this stage. If you do this, you should apply the filtering step described below at this stage, which will make the interpolation work better. (And then you will skip the filtering at the later stage.)
- If your data were recorded without a reference (usually this is only for the BioSemi ActiveTwo system), you may receive a warning that strongly encourages you to reference the data now. Do not do it. You will reference the data at a later step.
- Recommended: Save this dataset as a file
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If there are multiple data files (e.g., one per trial block), combine them into a single dataset.
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If appropriate, shift the stimulus event codes in time to account for any consistent mismatch between the time of the event code and the actual stimulus onset time
- All LCD displays interpose a constant delay between the time that the video information arrives from the computer’s video card and the time that the image is presented on the screen. This delay cannot be detected by the computer and cannot be determined reliably from the manufacturer’s specifications. It must be measured with some kind of photosensor. This delay is often greater than 25 ms, so it must be accounted for.
- Almost all video displays (LCD and CRT) have a delay that depends on the vertical position of the stimulus on the display. This delay is typically ~15 ms for the bottom of the display relative to the top (assuming a refresh rate of 60 Hz). If you are using stimuli at very different vertical locations in your different experimental conditions, you should measure the delay separately for the different locations and adjust accordingly. For large stimuli that are vertically centered, we measure the delay in the vertical center of the display.
- Delays may also occur for stimuli in other modalities. The delay should be measured and, if substantial, accounted for by shifting the event codes.
- Make sure that you shift only the stimulus event codes and not the response event codes (unless the there is also a delay for the responses). Use a positive shift value because the event code needs to be shifted later in time (because the stimulus occurred after the event code).
- ERPLAB’s function for shifting event codes creates a CSV file showing how each event code was shifted. You should look at this file to verify that the shifting was correct.
- It’s also important to verify that the delay is consistent (±1 sample period). If it is not consistent, there is probably a problem with the stimulus presentation script.
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If desired, downsample your data to a lower sampling rate
- My lab typically records at 500 Hz and then downsamples to 250 Hz. This gives us a higher sampling rate if we ever need it, but downsampling to 250 Hz makes the subsequent data processing faster and the data files half as large.
- Note that EEGLAB’s pop_resample routine will automatically apply an appropriate antialiasing filter prior to the resampling process.
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Apply a bandpass filter to the EEG and EOG channels
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We ordinarily use a non-causal Butterworth impulse response function, 0.1–30 Hz half-amplitude cut-off, 12 dB/oct roll-off.
- Some researchers prefer a lower cutoff for the high-pass filter (e.g., .05 Hz or .01 Hz), especially when looking at slow components like the late positive potential. However, we find that 0.1 Hz works best in most cases. Do not use anything higher than 0.1 Hz unless you really know what you’re doing!
- You should apply the option for removing the DC offset in the data prior to filtering. This can reduce the edge artifacts that occur at the beginning and end of each recording period.
- If extensive 60 Hz noise is present, you can apply the cleanline plugin (Mitra & Pesaran, 1999; see Bigdely-Shamlo et al., 2015 for important details about implementing this tool). If cleanline doesn't work well for you, you can try the newer Zapline method (de Cheveigné, 2020; Klug & Kloosterman, 2022). Alternatively, you could decrease the low-pass frequency to 20 Hz and/or increase the slope of the low-pass filter to 48 dB/octave (which requires doing the low-pass and high-pass filtering as separate steps).
- If you have also recorded other signals (e.g., a photosensor), you may not want to filter those channels (or you might want different filtering parameters for those channels).
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We ordinarily use a non-causal Butterworth impulse response function, 0.1–30 Hz half-amplitude cut-off, 12 dB/oct roll-off.
- Add channel location information specifying the 3-D locations of the electrodes.
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Perform channel operations to create bipolar channels (and to reference the data if they were not referenced during the recording).
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Create a bipolar HEOG channel (HEOG-left minus HEOG-right or vice versa)
- If you do not have HEOG electrodes, you can use F7 minus F8 (or just skip this step).
- If your data already contain a bipolar HEOG channel, you should skip this step.
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Create a bipolar VEOG channel (VEOG-lower minus the closest electrode that is above the eyes). For example, if the VEOG-lower electrode is under the left eye, the FP1 signal would ordinarily be subtracted from the VEOG-lower signal.
- If your data already contain a bipolar VEOG channel, you should skip this step.
- Keep the original, monopolar EOG channels, which will be important for ICA.
- Make sure that the channel location information is preserved by the Channel Operations routine.
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If your data were not recorded with a reference, reference the data now.
- In some systems (e.g., BioSemi ActiveTwo), the data saved to disk are not referenced and you should perform referencing now. However, if your data were referenced during recording, do not re-reference now. The re-referencing will be performed later, after artifact correction.
- In most labs that use the Brain Products ActiCHamp system, the data are already referenced at this point. However, our lab has a custom version of the data acquisition system in which the data are not referenced. Our lab therefore references at this point (and we re-reference later, after artifact correction).
- If you are referencing now, use a single electrode site as the reference. If a combination of sites is desired in the long run (e.g., the average of all sites, the average of the mastoids), you will re-reference to that combination later.
- It doesn’t really matter what site is used as the reference at this point. My lab uses P9.
- Recommended: Save the resulting dataset as a file. We call this dataset the pre-ICA dataset .
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Create a bipolar HEOG channel (HEOG-left minus HEOG-right or vice versa)
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View the EEG to make sure everything looks okay and to identify channels that require interpolation. These channels will be left out of the ICA decomposition process. The actual interpolation will be done after the ICA correction has been performed.
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To identify channels that should be interpolated:
- Visually inspect the EEG on both short (e.g., 5-second) and long (e.g., 60-second) time scales. This video demonstrates how to perform an initial visual inspection of continuous EEG data https://doi.org/10.18115/D5V638 .
- If the voltage drifts around or there are many sudden changes in voltage, that channel should be interpolated.
- If a channel is fine for most of the session but shows occasional periods of large deflections, this channel can be interpolated after epoching but limited to epochs in which the large deflections occur (as determined with the artifact detection procedures).
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If a channel shows a lot of high-frequency noise, it may not actually need to be interpolated.
- If the main dependent variable will be the mean voltage over some time range (e.g., 200-300 ms for N2pc or 300-500 ms for N400), high-frequency noise is not usually a problem. The best way to tell if it will be a problem is to look at the standardized measurement error (SME). If the SME for that channel is >2 SD beyond the mean SME of the other channels (excluding EOG, Fp1, and Fp2), then the channel should be interpolated. If the channel is the main channel for data analysis, you could interpolate if it is >1.5 SD beyond the mean.
- If there is a lot of high-frequency noise, the signal may also be corrupted in this channel. To see this, make a note to check the averaged ERP for that channel and surrounding channels after the averaging process. If the channel looks quite different from the surrounding channels, the signal is probably corrupted and the channel should be interpolated (which will require going back to this stage and repeating all the subsequent processes.
- If the main dependent variable will be a latency value and/or a peak-related variable, high-frequency noise is more likely to be a problem. You can confirm this by computing the bootstrapped SME when you get to the averaging step.
- Save information about channels that should be interpolated in an Excel file. That makes it possible to repeat the processing with a script.
- If a given channel misbehaves only occasionally, save this information the Excel file that controls artifact detection.
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To identify channels that should be interpolated:
Step 2: ICA-Based Artifact Correction
- Make a copy of the pre-ICA dataset . We will use this new dataset for the ICA decomposition. This new dataset is called the ICA decomposition dataset .
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Apply the following operations to the
ICA decomposition dataset
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Bandpass filter with half-amplitude cutoffs at 1 and 30 Hz, 48 dB/octave
- It’s OK that we’ve double-filtered the data. The original filtering is so much milder that it will be dwarfed by the new filter.
- If your previous low-pass cutoff was at 20 Hz, use 20 Hz here as well
- If your previous low-pass slope was 48 dB/octave, just do a high-pass filter at this stage (1 Hz, 48 dB/octave).
- Note: It is important that this filtering is done before the following steps. Some of the following steps introduce discontinuities in the EEG data, and those can lead to edge artifacts if the filtering is applied later.
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Resample the data at 100 Hz.
- This is not strictly necessary, but it makes the ICA decomposition faster.
- Don’t resample if the recording was brief. You need enough data to train the ICA decomposition routine. See the chapter on artifact correction for details on how much data is necessary.
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Delete break periods, because the EEG is often “crazy” during breaks, which degrades the ICA decomposition.
- A break is defined as a period of at least X ms without an event code, where X is some reasonable value (e.g., 2000 ms, assuming that you never have 2000 ms between event codes except during breaks).
- You can tell it to ignore certain event codes. You should always exclude boundary events. You may also want to exclude response events (in case the subject makes button presses during the breaks).
- You need a buffer at the edges of the break periods so that you do not cut into your eventual epochs (e.g., 1500 ms at the beginning of the break and 500 ms at the end of the break).
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Delete periods of “crazy” EEG (wild deflections, beyond what you see with ordinary artifacts).
- This can ordinarily be done using ERPLAB’s Artifact rejection (continuous data) routine.
- When setting the parameters, make sure that you are mainly rejecting segments of data with "crazy" EEG and are not rejecting segments with blinks or other ordinary artifacts.
- You should ordinarily exclude the EOG channels. If you include these channels, you may need a rejection threshold that is too high for the EEG channels. For subjects with unusually large blinks, you may also need to exclude Fp1, Fp2, or any other channels that are very close to the eyes.
- For most subjects, a threshold of 500 µV and a window size of 1000 ms works well. However, you should visually inspect the results and adjust these parameters if necessary. If blinks exceed the threshold, you will need to increase the threshold (or perhaps exclude Fp1, Fp2, or other channels with huge blink activity). The final parameters should be stored in an Excel spreadsheet for use in scripting.
- Check the box labeled Join artifactual segments separated by less than and put 1000 in the corresponding text box.
- Note that this deletion of segments with "crazy" EEG is designed only the improve the ICA decomposition. Once the ICA weights are transferred back to the pre-ICA dataset to create the post-ICA dataset (see below), these segments will be present in the data. You will later epoch the post-ICA data and apply ordinary artifact detection to mark and eventually excluded any epochs that contain wild voltage deflections. This way, you will have an accurate count of the number of trials excluded because of artifacts.
- Recommended: Save the final version of the ICA decomposition datase t as a file.
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Bandpass filter with half-amplitude cutoffs at 1 and 30 Hz, 48 dB/octave
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Perform the ICA decomposition process on the
ICA decomposition dataset
.
- Make sure that ‘ extended’, 1 is set (it should be set by default). This allows ICA to detect sub-Gaussian components, such as line noise and slow drifts.
- Exclude the bipolar EOG channels (because we will use these later to see the blinks and eye movements). If your dataset does not contain unipolar EOG signals, the ICA decomposition will still work reasonably well.
- Exclude “bad channels” that will be interpolated.
- If the ICA crashes or fails to converge, check the dataset to see if you have a lot of very short segments between boundary events. If so, you may need to alter your procedures for deleting periods of "crazy" EEG (e.g., by increasing the value for Join artifactual segments separated by less than ).
- Recommended: Save the result as a new file.
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Examine the components (especially the scalp maps) to make sure that the decomposition worked correctly. You should have 1-2 channels corresponding to blinks (and possibly vertical eye movements) and 1-2 channels corresponding to horizontal eye movements.
- My lab doesn’t ordinarily remove components corresponding to other artifacts, but this could be done when necessary for EKG artifacts and perhaps others.
- Determine which components correspond to artifacts that should be removed. This is done by both examining the scalp maps and comparing the time course of the components with the time course of the EOG signals. This information should be stored in a spreadsheet so that it can be used in scripts.
- Transfer the ICA weights from the ICA decomposition dataset to the pre-ICA dataset . The result is called the post-ICA dataset .
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Remove the independent components corresponding to the artifacts.
- Recommended: Save the result as a file.
- Visually inspect the corrected data to make sure that the correction worked properly.
Step 3: Post-ICA EEG Processing (starting with the post-ICA dataset)
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Re-reference the data
- My lab’s current preference is the average of P9 and P10, with the average of the left and right mastoids as a second best alternative. It is usually best to use whatever is most common in your area of ERP research. For example, we use the average of all sites as the reference when we look at the N170 elicited by faces, because that is the most common reference in that research area. This makes it easier to compare ERPs across studies (because a different reference can make the waveforms and scalp distributions look radically different).
- Also create bipolar HEOG and VEOG from the ICA-corrected EOG channels and look at them to assess the effectiveness of the artifact correction.
- Keep the uncorrected bipolar HEOG and VEOG signals, which we will use for detecting blinks and eye movements that occurred near that time of stimulus onset and may have interfered with perception of the stimulus.
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Perform the interpolation for the “bad channels” that were identified earlier.
- Non-EEG channels (e.g., EOG channels, a photosensor channel, a skin conductance channel) should be ignored in the process of computing interpolated values.
- Note that interpolation should ordinarily be performed after high-pass filtering.
- If you are using the average of all sites as the reference, you should either perform the interpolation before referencing or exclude any to-be-interpolated sites from the reference.
- Add an EventList to the dataset
- Run BINLISTER to assign events to bins
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Extract bin-based epochs
- Important: Use ERPLAB’s tool (Extract bin-based epochs), not EEGLAB’s tool (Extract epochs). The subsequent ERPLAB operations will not work correctly if you use EEGLAB’s tool.
- Our standard epoch is from -200 to +800 ms. A longer prestimulus is used if we will be doing frequency-based analyses or if we want to maximize trial-to-trial stability of the signal (e.g., for decoding, which is extraordinarily sensitive to trial-to-trial variability).
- Baseline correction is ordinarily applied at this step.
- Recommended: Save the epoched dataset as a file.
Step 4: Artifact Detection
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General procedure for a given type of artifact
- Start with default detection parameters
- Apply to data
- Check number of trials detected
- Scroll through data to determine whether the parameters were effective
- If the parameters were not effective, update them and try again until effective parameters are found
- The parameters should be stored in a spreadsheet for future scripting.
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Standard artifacts to detect
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Blinks and eye movements that might interfere with the perception of the stimulus
- Test for blinks in the uncorrected bipolar VEOG channel and test for eye movements in the uncorrected HEOG channel
- Use the step function with a window size of 200 ms and a step size of 10 ms
- The test period should start at -200 ms (because vision is functionally suppressed for ~100 ms after the blink is complete, so we want to detect blinks even if they ended shortly before stimulus onset)
- The test period should be at least 200 ms and should terminate at or after the offset of the stimulus
- Start with a threshold of 50 µV for blinks and 32 µV for eye movements (which corresponds to a 2° rotation of the eyes)
- You can often look at the averaged EOG signals to see if you’ve successfully removed these artifacts.
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General C.R.A.P. that increases measurement error
- Apply to all channels except for the uncorrected HEOG and VEOG channels
- Use both the absolute voltage threshold and moving window peak-to-peak algorithms; they occasionally catch different trials
- The test period should typically encompass the whole epoch.
- 150 µV is a good starting threshold.
- The goal is to reduce measurement error, which you can quantify by looking at the SME. When you discard a trial because of C.R.A.P., you reduce trial-to-trial variability, which decreases measurement error. However, you also reduce the number of trials, which increases measurement error. The SME takes both into account and tells you whether, when both factors are considered, the measurement error is better or worse.
- You can tolerate more C.R.A.P. in a given channel if that channel will not contribute to your main analyses (e.g., if your analyses will be limited to other channels). In many cases, most of the channels are used only when plotting scalp maps. However, if you will be re-referencing after artifact detection, any channels that are part of the reference are important.
- Note: Use a different flag for each type of artifact. This makes it possible to track how many artifacts of each type were flagged.
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Blinks and eye movements that might interfere with the perception of the stimulus
- The number of trials with versus without artifacts should be recorded. We do this aggregated across conditions (i.e., collapsed across bins). If the percentage of rejected trials is greater than 25%, my lab always excludes the subject from the final analyses. (We raise this threshold to 50% for studies of psychiatric and neurological conditions.) A different threshold for exclusion may be appropriate for other kinds of research. However, it is important for the exclusion criterion to be set prior to looking at the data.
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After a participant’s data have been fully processed in this way (including visualizing the data and saving all the participant-specific analysis parameters in one or more spreadsheets), the participant’s data should be reprocessed with a script
- This should yield the same result, but it can avoid errors that may occur in manual processing
- The ICA decomposition process does not need to be repeated when the data are re-processed with a script. That is, the weights can be transferred from the ICA decomposition dataset created during the manual processing.
References
Bigdely-Shamlo, N., Mullen, T., Kothe, C., Su, K.-M., & Robbins, K. A. (2015). The PREP pipeline: Standardized preprocessing for large-scale EEG analysis. Frontiers in Neuroinformatics , 9 . https://doi.org/10.3389/fninf.2015.00016
de Cheveigné, A. (2020). ZapLine: A simple and effective method to remove power line artifacts. NeuroImage, 207, 116356. https://doi.org/10.1016/j.neuroimage.2019.116356
Klug, M., & Kloosterman, N. A. (2022). Zapline-plus: A Zapline extension for automatic and adaptive removal of frequency-specific noise artifacts in M/EEG. Human Brain Mapping, 43(9) , 2743–2758. https://doi.org/10.1002/hbm.25832
Luck, S. J. (2014). An Introduction to the Event-Related Potential Technique, Second Edition . MIT Press.
Mitra, P. P., & Pesaran, B. (1999). Analysis of Dynamic Brain Imaging Data. Biophysical Journal , 76 (2), 691–708. https://doi.org/10.1016/S0006-3495(99)77236-X