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![Week 7- fMRI processing
Lecture/ Lecture reading:
The following notes integrate the lecture slides with the reading
Chapter 4, Preprocessing section (“Analyzing Data from Functional Imaging”, pp. 65-68).
Student’s Guide to Cog Neuroscience
Preprocessing: eliminates variability in the BOLD signal that is not due to the task
1. Slice Timing
Can be interleaved, ascending, or descending
SPM assumes each scan is instantaneous
● Data not collected at the same time but want to make it seem like we did so we
correct for this
● Only needed when temporal dynamics of BOLD responses are important and TR is
small enough to permit interpolation (TR< 3 second)
2. Realignment
● People move around in scanner (pitch, roll, yawn)
● Realignment adjusts for this
● There are ways to prevent movement of subjects, including reminding them!
3. Coregistration
● Brain activation (fMRI) data is aligned with a structural image
4. Normalization
● Wrap each subject’s brain to a template (average) brain
○ Basically nonlinear transformations to get all brains to “fit” in a standard
brain
5. Smoothing
● Still some variability left before doing this step
● Replace intensity value of a voxel with a weighted average of its original value plus
the value of neighboring voxels
○ [voxel: volume-based unit--in imaging research the brain is divided into may
thousands of these]
● Smoothing spreads the activity across voxels: some voxels may be enhanced
whereas others may be reduced
● Comes with the cost of spatial precision
○ Do not use if brain region is very small (1-2 voxels)!](https://image.slidesharecdn.com/makki-161218102539/85/Psych-302-Midterm-Study-Guide-13-320.jpg)
Psych 302 Midterm Study Guide
- 1. Ibtihal Makki Section 007 Psych302 Midterm Study Guide Week 1- Introduction Lecture/ Lecture reading: ● Cognitive Neuroscience focuses on the neuronal mechanisms by which various mental processes occur. ● Keys to Conducting an fMRI study a. Design behavioral task: Isolate psychological process that you are interested in b. Modify the behavioral task to make it appropriate for an fMRI study c. Analyze behavioral and fMRI data ● Experimental Design (Ch. 6, “Experimental Design in Psychological Research) a. Variables are carefully controlled b. 4 Goals i. Describe i.e. early astronomers describing the positions and motions of stars ii. Predict i.e. through careful observations and documentation, later astronomers because skillful at predicting planetary stellar motion iii. Determine causes i.e. Newton’s laws of motion and Einstein’s special and general theories of relatively thereby explaining the causes of stellar motion iv. Explain i.e. A full explanation is not yet elusive because using gravity as an explanation is merely a label for the phenomenon and doesn’t explain how gravity works. c. 3 major types i. Controlled (“true”) ● RANDOM ASSIGNMENT, identical experimental conditions, independent variable, dependent variable. ii. Correlational ● Relies on patterns of co-occurrence or correlations between events ● Classical ex- cigarette smoking and cancer; problem: “factor x” iii. Descriptive ● Seek to describe an aspect of the world as it is ● I.e- which part of the brain is activated when a person performs a mental calculation d. Study designs i. Between-subjects ● Each group is in ONE condition ONLY= independent group design
- 2. ii. Within-subjects ● Everysubject is tested in EVERY condition= repeated measures design ● Advantage: smaller number of subjects required ● Disadvantage: demand characteristics- subjects are not as naive about the experimental manipulation, carryover effects, order effects e. Confounds i. Clever Hans ● Horse- became famous following demonstrations in which he performed simple addition and subtraction by tapping his hoof on the ground ● Problem: it was discovered that Hans became adept at picking up subtle movements on the part of the questioner that cued him to stop tapping his hoof f. Ethical Considerations i. Informed consent ● Subjects given an accurate description of their task, risks, allowed to leave experiment ii. Debriefing ● Following experiment, subject given an explanation of the hypothesis and methods iii. Privacy/Confidentiality ● Subject information that is collected is coded and stored in a way that leaves identities confidential iv. Fraud ● Data should not be fabricated and false data/analyses/conclusions should never be knowingly published. g. Analyzing Data i. Measurement error ii. Significance testing ● Reproducibility of experiments in psychological science ● Distraction slides included in notes under “Week 2” Lab Readings Botvinick et al. (1999). “Conflict monitoring versus selection-for-action in anterior cingulate cortex ● Hypothesis: 2 Possible function of ACC: 1. Conflict Monitoring
- 3. 2. Selection foraction The ACC is involved in regulating attention and functions via conflict monitoring ● Basic Procedure: Used fMRI and flanker test (arrows) to measure brain activation in the ACC ● Main Result: ACC had increased activation during the CI trails high levels of conflict; weak selection for action→ evidence supports conflict-monitoring theory. Conclusion: The role of the ACC is conflict detection ● Limitations: Feature repetitions only occur on cC and iI trials: Maybe CSE is really just a learning effect. Mental rotation confounds. Mayr et al. (2003). “Conflict adaptation effects in the absence of executive control” ● Hypothesis: The conflict adaptation effect is due to repetition priming and will be: ○ present when the target and flanker are repeated ○ absent when either the target or flanker change ● Basic Procedure: Study 1: Which direction does the central arrow point? Measure cC, cI, iI, and iC trials: Determine if (cI-cC)>(iI-iC) as a function of repetition Study 2: Same question; to prevent stimulus repetitions, alternated between L/R and U/D arrows ● Main Results: Study 1: Conflict adaption only in repetition trials: consistent with hypothesis; contradicts conflict monitoring model Study 1: No observed conflict adaption: consistent with hypothesis; contradicts conflict monitoring model ● Limitations: mental rotation confounds Week 2- Conflict Adaptation Lecture/ Lecture reading: ● Coping with Distractions: we are constantly inundated with stimuli and need to selectively attend to certain tasks while ignoring to “distractors” ● Laboratory tasks for investigating distraction ○ Stroop-like task (green/red) ■ Often have many trials ○ Flanker task (arrows) ○ Simon task (left/right) ● Congruency effect: reaction times (RT) for subjects is faster during congruent trials when compared to incongruent trials in selective attention tasks. ● Congruency sequence effect: the congruency effect is smaller in trials following incongruent trials when compared to congruent trials
- 4. ● Mechanisms underlyingCSE: ○ Selection for Action: -shifting attention to something ■ Perceptual expectation ■ Conflict monitoring ● ACC/conflict monitoring Botvinick et al 1999 investigated if the ACC underlies selection for action or whether it triggers it through conflict monitoring **Explained above in Week 1 Lab readings** ■ Negative effect ○ Response Inhibition: inhibit response primed by distractor ● Influences on the CSE: Learning/memory processes ○ Feature repetitions: (Mayr 2-AFC flanker task) only occur on cC and iI trials: Maybe CSE is really just a learning effect. ○ Contingency learning biases- participant learn to prepare the congruent response signaled by the distracted (i.e. in Ullsperger’s 9-AFC digit flanker task) because it is more likely to be correct and so can lead to a confound driven CSE ● Mental rotation confounds ○ In experiments that utilize arrows as stimuli, it is important to realize that each arrow stimulus is a mental rotation of the other arrow stimuli. ● CSE without confounds Reading: Schmidt & Weissman (2014). “Congruency sequence effects without feature integration or contingency learning confounds” ● Hypothesis: A CSE can be observed without feature repetition, contingency learning, or mental rotation confounds ● Basic procedure: 4-AFC task → a pair of 2-AFC tasks ○ Example: “left-right” versus “up-down” Alternated between these 2 tasks on every trial ○ Each task performed with a different hand (index & middle fingers) Presented congruent/incongruent stimuli equally often in each task Counterbalanced congruent/incongruent trials in every block ○ Ensured equal numbers of cC, cI, iC, & iI trials ● Main result: A CSE can be observed independent of feature repetitions and contingency learning confounds ● Limitations: This suggests that a control process influences the CSE, but does not reveal which one: (Selection for Action or Response inhibition) Class experiment: Goal- Distinguish between Selection for Action and Response inhibition accounts
- 5. Method: vary thetemporal interval separating the distractor from the target Task: indicate the direction of the word specified by the large target word left, right, up, down) and not the preceding distractor. ● If the selection for action account is correct, there should be no congruency effect after incongruent trials because with long intervals separating the distractor and target, it should be the case that subjects are able to shift their attention to the target, entirely. ● If the response inhibition account is correct, there should be an observed negative or reverse congruency effect after incongruent trials because with long intervals separating the distractor and target, it should be the case that subjects are able to inhibit the response signaled by the distractor, fully. Week 3-Basic Statistics Lecture/ Lecture reading: Reading- Statistics Review 5: Comparison of Means The following notes integrate the lecture slides with the reading ● Stats describes how likely a particular sample mean is to come from the distribution associated with the null hypothesis ● P-value is the probably that the sample mean came from that null distribution (one- or two-tailed tests) ● Comparison of a single mean with a hypothesized value ○ To compare a mean value from a sample mean to an external standard (i.e hemoglobin concentrations in UK males to the standard). ● Comparison of two means arising from paired data ○ Paired data arise in matched case-control studies or repeated measures studies ● Comparison of two means arising from unpaired data ○ Comparison of two means arising from unpaired data (i.e. comparison of data from two independent groups) ● Assumptions and limitations ○ Unpaired t-test relies on the assumption that the data from the two samples are both normally distributed ● Main effects and Interactions ○ Main effect: effect of a single independent variable on a dependent variable; all other independent variables are ignored ○ Interaction: the different conditions for an independent variable produce different results depending on which condition you consider for a second independent variable (difference of differences).
- 6. ○ The Youtubevideo posted by professor weissman on the canvas site is very helpful (https://www.youtube.com/watch?v=OE46w0RqmQA) Lab Readings Ullsperger et al. (2005, skip Experiment 1). “The conflict adaptation effect: It’s not just priming” ● Hypothesis: Their experiment would reveal a CSE on trial sequences not involving stimulus repetitions ● Basic procedure: Indicate the underscored target digit (1-9), which was surrounded by two identical flanker digits on either side (presented at the same time) ● Results: CSEs were demonstrated by the experimentation ● Limitations: Contingency learning bias multiplied # of compatible trials by 8, made it possible for subjects to guess that 50% of the trial would be compatible Kunde & Wuhr (2006, skip Experiment 2). “Sequential modulations of correspondence effects across spatial dimensions and tasks ● Hypothesis: Repetition/alternation account exists if sequential modulation of SR compatibility effects are absent and response conflict account exists if sequential modulations of SR compatibility effects persist. ● Basic procedure: 4-AFC prime-probe task with left, right, up, and down arrows ● Results: Observed a CSE even in trials without exact feature repetitions or contingency learning biases ● Limitation: Arrow stimuli = mental rotations of the same arrow stimulus Week 4-Scientific Writing Lecture(no lecture slides) Lecture reading: Commentary, the art of writing science The elements of Scientific Style: ● Word choice ○ Do not invent new words or phrases, use words already in the literature. ○ Avoid abbreviations (i.e. use ‘‘the forward rate constant’’ rather than ‘kf’) ○ Avoid arbitrary names (i.e. use ‘‘protein dilution buffer’’ instead of “buffer A”) ○ Use formal, precise words rather than colloquial, ambiguous ones (i.e. ‘‘these data show’’ is less precise than ‘‘these data indicate) ○ Use present tense when possible ● Sentences ○ Don’t use passive voice ○ Vary sentence length across a paragraph ○ Symmetrical language, parallel structures within and between sentences ● Paragraphs
- 7. ○ First sentence:tell reader what they will expect ○ Discuss a single idea per paragraph ○ Transition logically between sentences and between paragraphs The elements of a scientific paper ● Title: highlight the main result of the study, not the main effort ● Introduction ○ One purpose: convince readers to read the paper ○ Convince readers the question is important and give a reason for them to care ○ Prime readers to expect an answer ○ Keep the intro short ○ Start broad and progress into specific details ● Results ○ Provide conceptual tools to understand the results ○ Minimal discussion ● Discussion ○ Reiterate point blatantly ○ Speculate on implications ○ Start specific and give wider ideas ● Methods ○ Every necessary detail were someone to attempt to reproduce your work ○ Watch tenses here too ● Figures/captions ○ Clearly and concisely tell the reader what you expect them to learn from figures in the caption ● Abstract ○ The entire paper in brief ○ Should start with a blunt sentence describing the broad field ○ Followed by as sentence describing the specific problem at hand ○ Next sentence states what the reader should expect to learn ○ Briefly describe results and conclusion Most important rule: ignore any and all rules if doing so makes the paper easier to read ● Purdue reading, main points: ○ Use plain, concise and clear language ○ Psychology bases arguments on evidence based reasoning ○ Use APA format No Lab readings Week 5- What is fMRI?
- 8. Lecture/ Lecture reading: Thefollowing notes integrate the lecture slides with the reading “What is fMRI?” ● fMRI is a technique used to measure brain activity ● When a brain area is more active, it consumes more oxygen and to meet this increased demand, blood flow increases to that area ● Advantages: 1. Non-invasive and doesn’t use radiation (safe) 2. Excellent spatial and good temporal resolution 3. Easy for experimentation to use ● Key: the signal from hydrogen nuclei varies in strength depending on surroundings ○ Provides a means of discriminating between gray matter, white matter and cerebrospinal fluid in structural images of the brain ● BOLD signal ○ An indirect measure of neural activity ○ Since blood oxygenation varies according to the levels of neural activity, differences in magnetic properties of hemoglobin (diamagnetic when oxygenated and paramagnetic when deoxygenated) can be used to detect brain activity Ch. 4 “The imaged brain” from the “Student’s Guide to Cognitive Neuroscience” by Ward ● Structural vs functional imaging methods ● Computerized tomography (CT) ○ Construed according to x0ray absorption in different types of tissue ■ Typically used only in clinical settings (diagnosing tumors, identifying hemorrhaging, etc.) ● Advantages of MRI (some of this is similar to the information from the reading above): ○ Does not use ionizing radiation, is safe ○ Provides better spatial resolution (individual gyri discrete) ○ Provides better discrimination between white and gray matter ○ Can be adapted for use in detecting blood oxygenation changes associated with neural activity (fMRI) ● Structural MRI is used to study brain anatomy while Functional MRI is used to study brain function ● Diffusion tensor imaging (DTI) ○ MRI based methods for imaging the axon tracts that form the white matter of the brain ○ Measures density and motion of water traveling along myelin-covered axons ○ Water normally diffused in all directions but since myelin has a lipid boundary, that biases water to move along the length of the axon
- 9. ○ Measuring thismovement can create images of white matter tracts in brain ● Basic physiology underpinning functional imaging ○ Brain consumes a fifth of the body’s oxygen uptake, does not store oxygen and little glucose ○ Blood supply to an activated region must increase to meet the demand ○ Brain is always physiologically active ● PET ○ Uses a radioactive tracer injected into the bloodstream ○ Greater blood flow i a region indicated by a greater signal being emitted by the racer in that region ○ Usually oxygen-15 or fluorine-18 ● More fMRI information ○ The way the BOLD signal evolves over time in response to an increase in neural activity is called the hemodynamic response function (HRF) ○ HRF has 3 phases: 1. Initial dip 2. Overcompensation 3. Undershoot ● Cognitive theory ○ Cognitive subtraction: by comparing the activity of the brain in a task that utilizes a particular cognitive component to the activity of the brain in a baseline task that does not, it is possible to infer which regions are specialized for that particular cognitive component ○ Problems: assumption of pure insertions and interactions make imaging data ambiguous ● Parametric vs categorical design ○ Continuous vs categorical variables ● Functional integration: refers to the way in which different regions communicate with each other ○ It is likely to be essential for a full understanding of how cognition is linked to the brain The rest of this reading is described in week 6 material since it relates to the lecture notes from that week! ● Sports and head injury ○ Concussions and subconcussive hits in many sports are suggested to be associated with chronic traumatic encephalopathy (CTE) ■ Buildup of tau protein, problems with memory, concentration, depression, anger ■ Stricter policies implemented in some sports
- 10. Lab readings: Parvizi etal. (2013). “The will to persevere induced by electrical stimulation of the human cingulate gyrus” ● Hypothesis: (1) Activation of the ACC will induce autonomic, emotional, and cognitive experiences defined as the “will to preserve” and (2) activity in the ACC will modulate activity in a larger network of connected regions ● Methods: multimodal data acquisition: electrical stimulation and prompting question, resting fMRI, intracranial implementation, electrical brain stimulation, heart rate analysis, and patient reports ● Results: Emotional salience network seeded from location of stimulation in both patients. ● Implications: structural brain anatomy and environmental influences on plasticity for differences in coping Coleshill et al. (2004). “Material-specific recognition deficits elicited by Unilateral Hippocampal Stimulation.” ● Hypothesis: unilateral stimulation-induced hippocampal disruption produces impairments on delayed RM tasks which supports the material-specific laterality of hippocampal function with respect to RM. ● Methods: electrode implantation, stimulation, recognition tests (faces, objects, words) ● Results: double disassociation for the hippocampus’ role in delayed RM: left side, word RM and right side: face RM deficits. ● Limitations: Small and specific sample size; generalization to a larger population? Oliver Sacks (1970). “The Man who mistook his wife for a hat”, pages 7-15. ● Dr. P: musician of distinction (teacher) ● Perfectly healthy except problems identifying visual images: faces particularly ● Recognized distinctive features (i.e. jaw/teeth) ● Dr. Sacks examined him: tests with shapes and pictures--couldn’t tell the difference between his shoe and foot ● Visualization was actually fine but his interpretation of faces/scenes: impaired ● “I think that music, for him, had taken the place of image” -Dr. Sacks Week 6- How to design fMRI studies Lecture/ Lecture reading: The following notes integrate the lecture slides with the reading Ch. 9, “Experimental Design for fMRI”, Huettel et al. (2009). Functional MRI. ● Experimental design/ Basic principles
- 11. ○ Functional connectivity:pattern of functional relationships among regions, inferred from common changes in activation over time; may reflect direct or indirect links ○ Other terms: research hypothesis, experiment, experimental design, efficiency, variable, independent variables, conditions, dependent variables ○ Categorical variables: discrete ○ between/within-subject manipulation (explained in week 1) ● Hypothesis: ○ 3 distinct levels: ■ most specific level are about hemodynamic activation ■ second class are about neuronal activity ■ Third is the psychological hypothesis (most difficult to construct) ● Terms to be familiar with: theory, experimental condition, control condition, epiphenomenal(as it related to correlational interpretations) ● Confounding factors: property that covaries with the independent variable within the experiment but could be distinguished from the independent variable using a different design. ○ if an experiment has two conditions (experimental and control; they should be as similar as possible ○ Terms to be familiar with: Subtraction, randomization, counterbalancing ● Good practices in fMRI design: 1. Evoke cognitive processes of interest 2. Collect as much data as possible from each subject 3. Collect data from as many subjects as possible 4. Choose stimulus condition and the timing to evoke maximal changes in the cognitive process of interest 5. Organize timing of stimuli so that successively elicited processes of interest are minimally correlated with each other 6. Obtain measurements of subjects’ behavior if possible Event-Related vs. Blocked designs ● Blocked design: separation of experimental conditions into two distinct blocks so that each condition is presented for an extended period of time ○ Consider the length of task blocks for the research question you are exploring ○ Alternating design: block design in which two conditions are presented one after another for the duration of the experimental run ○ Control block: contains trials of control conditions ○ null task block: control block in which there is no task requirements for the subject (baseline) ○ Pros/cons:
- 12. ■ Pro: Blockeddesign very good for detecting significant fMRI activation, the signal to noise ratio should be maximized to the task frequency ■ Con: Relatively insensitive to the shape of the hemodynamic response ○ Having two block types: counterbalance the order across runs or subjects ■ Resulting signals mainly reveal differences in activity between the block types ■ Poor estimate of baseline ■ But maximizes our ability to detect differences in activity at the expense of detecting absolute activity ■ If include low-level baseline condition between blocks, signals reveal: activity for each block type and differences between blocks ● More efficient at detecting absolute activation but less efficient at detecting differences ● Event related: presentation of discrete, short-duration events whose timing and order may be randomized ○ Central assumption: neuronal activity of interest will occur for short and discrete intervals ○ Terms to understand: event, interstimulus interval, EEG, time-locking, signal averaging, ERPs ○ Epoch: time segment extracted from the larger series of images, usually corresponding to the period of time surrounding an event of interest ○ Averaged epch: result of averaging a large number of epochs that are time locked to similar events ○ Example used in class: cued stroop task, revealed a double dissociation ○ Linearity assumption: do things add up? ■ Sync each trial response to start of trial; not quite linear but good enough Design Types: ● Rapid unjittered event-related design (randomized trial order) ○ Examples: Kerns et al. 2004 (short, constant ITI needed to study conflict adaptation ● Rapid, jittered ER design ○ Example: Recognition memory, wagner et al. 1998 ● Communication between brain regions: Functional connectivity- ○ If activity in two regions is correlated across time, these regions may be communicating ○ Uses: flanker and stroop tasks
- 13. Week 7- fMRIprocessing Lecture/ Lecture reading: The following notes integrate the lecture slides with the reading Chapter 4, Preprocessing section (“Analyzing Data from Functional Imaging”, pp. 65-68). Student’s Guide to Cog Neuroscience Preprocessing: eliminates variability in the BOLD signal that is not due to the task 1. Slice Timing Can be interleaved, ascending, or descending SPM assumes each scan is instantaneous ● Data not collected at the same time but want to make it seem like we did so we correct for this ● Only needed when temporal dynamics of BOLD responses are important and TR is small enough to permit interpolation (TR< 3 second) 2. Realignment ● People move around in scanner (pitch, roll, yawn) ● Realignment adjusts for this ● There are ways to prevent movement of subjects, including reminding them! 3. Coregistration ● Brain activation (fMRI) data is aligned with a structural image 4. Normalization ● Wrap each subject’s brain to a template (average) brain ○ Basically nonlinear transformations to get all brains to “fit” in a standard brain 5. Smoothing ● Still some variability left before doing this step ● Replace intensity value of a voxel with a weighted average of its original value plus the value of neighboring voxels ○ [voxel: volume-based unit--in imaging research the brain is divided into may thousands of these] ● Smoothing spreads the activity across voxels: some voxels may be enhanced whereas others may be reduced ● Comes with the cost of spatial precision ○ Do not use if brain region is very small (1-2 voxels)!