A role of right middle frontal gyrus in reorienting of attention: a case study methods
Show snapshot details
On this page
This experiment, in seven questions
Jump straight to the part of the recipe you need. Data and provenance labels stay close to the action they support.
Shopping and prep list
What do I need before I start?
Biological model pending
Subject model for the experiment.
- Use
- confirm full cohort details in the source paper
Before you run
What should be confirmed before execution?
First confirmation
Species or subject information is missing.
Confirm before execution
Protocol does not list structured equipment.
Confirm before execution
This page shows passages quoted from the paper. Equipment, materials, times, and temperatures are hidden until the page is rebuilt from the full paper and checked by a reviewer. Check the paper before using this method.
Confirm before execution
Open the source paper before finalizing run-specific details.
Procurement checkpoint
Use source-stated vendors where present. Treat mapped products as sourcing options unless the page marks an exact source match.
Open quote workflowStep-by-step procedure
What do I do, in order?
Apparatus
Stimuli were presented on a 24″ liquid crystal display monitor, with a resolution of 1024 × 768 pixels and a refresh rate of 60 Hz, in a dimly lit room. A chin rest was used to maintain position of the participant's eyes 57 cm from the screen and to minimize head motion. Stimuli for the adaptive thresholding and Endogenous Cueing experiment were presented using MATLAB 7.4 (Mathworks, Natick, MA) and Psychophysics Toolbox (Brainard,; Pelli, ). Stimuli for Exogenous Cueing and Go/No-Go experiments were presented using Presentation (Neurobehavioral Systems, Berkeley, CA). Sustained fixation at the center of the screen was monitored using the ASL Eyetrak 6000 (Applied Science Laboratories, Bedford, MA) for 7 out of the 10 subjects for Attentional Cueing experiments. Eye tracking was not performed for the Response Inhibition experiment, since stimuli in those tasks were present...
Methods
Figure shows the extent of the cortical resection in the patient's brain. In Talairach space, the resection spanned a region that extended from the midline of the right hemisphere ( x = 0) to a lateral location of x = 50 mm. This included the right superior frontal gyrus (SFG), right middle frontal gyrus (MFG), while almost completely sparing the right inferior frontal gyrus (IFG). Caudally the resection extended from y = 23 mm to y = ~66 mm (anterior tip of the brain). Dorsally, the resection spanned the region between z = -4 mm and z = 50 mm (superior tip of the brain). The resection removed most of Brodmann areas (BA) 9, 46, as well as the dorsal portion of BA 10, in the right hemisphere.
Methods
Coronal slices taken 6 mm apart starting posteriorly at y = 22 and showing the extent of the tumor resection in the right hemisphere. The resection encompassed right superior frontal gyrus and right middle frontal gyrus, including Brodmann areas 9, 46, and 10. Right inferior frontal gyrus was almost completely spared. In Talairach normalized space, the resection extended from x of 0 (midline) to about 50 mm, y of 23 to y of 66 mm (anterior tip of brain) and z of -4 to z of 50 mm (superior tip of brain).
Healthy controls
Attentional cueing experiments. Ten normal volunteers (5 females) age-matched to the patient (31.8 ± 3.4; mean ± SD years) participated in the study. Subjects completed one of three attentional cueing experiments on three separate visits spanning approximately 1 week.
Exogenous cueing task
In this experiment participants were shown an exogenous stimulus (a white box) at one of two locations, to the left or right of fixation (see Figure ). This white box prior to the appearance of the Gabor patch served as the exogenous cue with 50% validity. The box was followed by a white fixation spot for a variable amount of time, i.e., inter-stimulus interval (ISI) of either 0, 50, 100, 250, 500 or 700 ms. This was then followed by the Gabor patch that appeared for 50 ms in the cued or non-cued location with 50% validity with respect to the cue. This was followed by a gray fixation spot that indicated the 1500-ms response period. Participants were instructed that the location of the white box cue was completely random and unrelated to the location of the subsequent grating patch. On every trial the subject's task was to indicate with a button press the orientation of the Gabor patch...
Exogenous cueing task with explicit reorienting
In addition to difficulty orienting to an exogenous stimulus, it is also possible that, at longer durations between cue and stimulus, when the effect of the exogenous cue has extinguished, the patient may have trouble reverting back to top-down control of attention. To test this specifically, we had our participants complete another exogenous cueing experiment, which involved an explicit reorienting cue at longer durations to allow the patient to reorient to top-down control of attention (Natale et al., ). We hoped that by explicitly instructing the patient to reorient and divide his attention between the two possible stimulus locations, he would be able to perform better at the orientation discrimination task for these longer inter-cue-stimulus duration trials. This task consisted of three trial types including: implicit exogenous cueing, exogenous cueing with explicit reorienting, a...
Eye-tracking data analysis
We confirmed that subjects fixated at the center of the screen while doing each of the three Attentional Cueing experiments by analyzing the eye-tracker data using ASL Results Plus™. Data from 4 sessions were excluded from analysis due to poor data quality. The remaining data (6 subjects for Endogenous Cueing, 5 for Exogenous Cueing, and 5 for Exogenous Cueing with Explicit Reorienting) were used to determine the percentage of fixation duration within a rectangular Area of Interest (AOI) of ±3° of visual angle around the fixation spot (Note the Gabor patch was presented at ±5.5°). The patient's eye tracking data were analyzed similarly and then compared to the average of the control group using the Single Bayesian Test.
Resting state fMRI
Structural and resting state functional MRI (rsfMRI) data were acquired on a GE MR 750 3-Tesla scanner using a GE 32 channel head coil. A high-resolution structural image was acquired using a magnetization-prepared rapid-gradient-echo (MP-RAGE) T1-weighted sequence with the following parameters: time to echo [TE] = 3.42 ms; time to repetition [TR] = 7 ms; time to inversion [TI] = 425 ms; flip angle = 7°; Phase Acceleration Factor = 2; slices with 1 × 1 × 1 mm voxels). rsfMRI data were obtained using an axial echo-planar imaging (EPI) sequence ( TE = 28.1 ms; TR = 2500 ms; flip angle = 77°; Phase Acceleration Factor = 2; 44 slices, each 3 mm thick, with 2 × 2 mm in-plane voxel resolution). Two runs with 134 volumes for each run were acquired for each participant (Data for the control group were acquired as part of a larger project that is outlined in Barnes et...
Measurement outputs
What raw and processed outputs should exist?
Analysis plan
How should the outputs become interpretable results?
Acquisition
Collect raw experimental outputs with enough metadata to preserve sample identity, condition, and timing.
inferred from protocolPreprocessing / cleaning
Review raw outputs for quality, remove unusable captures, and organize the data into a comparison-ready table or image set.
inferred from protocolScoring or quantification
Quantify the primary endpoint described in the methods before moving into any statistical comparison.
inferred from protocolStatistical comparison
Statistical method not yet structured for this page.
inferred from protocolReporting output
Report representative outputs alongside the summary comparison used to support the conclusion.
inferred from protocolSource and audit
What supports the facts on this page?
Evidence quotes (8)
Stimuli were presented on a 24″ liquid crystal display monitor, with a resolution of 1024 × 768 pixels and a refresh rate of 60 Hz, in a dimly lit room. A chin rest was used to maintain position of the participant's eyes 57 cm from the screen and to minimize head motion. Stimuli for the adaptive thresholding and Endogenous Cueing experiment were presented using MATLAB 7.4 (Mathworks, Natick, MA) and Psychophysics Toolbox (Brainard,; Pelli, ). Stimuli for Exogenous Cueing and Go/No-Go experiments were presented using Presentation (Neurobehavioral Systems, Berkeley, CA). Sustained fixation at the center of the screen was monitored using the ASL Eyetrak 6000 (Applied Science Laboratories, Bedford, MA) for 7 out of the 10 subjects for Attentional Cueing experiments. Eye tracking was not performed for the Response Inhibition experiment, since stimuli in those tasks were presented at the center of the screen.
Figure shows the extent of the cortical resection in the patient's brain. In Talairach space, the resection spanned a region that extended from the midline of the right hemisphere ( x = 0) to a lateral location of x = 50 mm. This included the right superior frontal gyrus (SFG), right middle frontal gyrus (MFG), while almost completely sparing the right inferior frontal gyrus (IFG). Caudally the resection extended from y = 23 mm to y = ~66 mm (anterior tip of the brain). Dorsally, the resection spanned the region between z = -4 mm and z = 50 mm (superior tip of the brain). The resection removed most of Brodmann areas (BA) 9, 46, as well as the dorsal portion of BA 10, in the right hemisphere.
Coronal slices taken 6 mm apart starting posteriorly at y = 22 and showing the extent of the tumor resection in the right hemisphere. The resection encompassed right superior frontal gyrus and right middle frontal gyrus, including Brodmann areas 9, 46, and 10. Right inferior frontal gyrus was almost completely spared. In Talairach normalized space, the resection extended from x of 0 (midline) to about 50 mm, y of 23 to y of 66 mm (anterior tip of brain) and z of -4 to z of 50 mm (superior tip of brain).
Attentional cueing experiments. Ten normal volunteers (5 females) age-matched to the patient (31.8 ± 3.4; mean ± SD years) participated in the study. Subjects completed one of three attentional cueing experiments on three separate visits spanning approximately 1 week.
In this experiment participants were shown an exogenous stimulus (a white box) at one of two locations, to the left or right of fixation (see Figure ). This white box prior to the appearance of the Gabor patch served as the exogenous cue with 50% validity. The box was followed by a white fixation spot for a variable amount of time, i.e., inter-stimulus interval (ISI) of either 0, 50, 100, 250, 500 or 700 ms. This was then followed by the Gabor patch that appeared for 50 ms in the cued or non-cued location with 50% validity with respect to the cue. This was followed by a gray fixation spot that indicated the 1500-ms response period. Participants were instructed that the location of the white box cue was completely random and unrelated to the location of the subsequent grating patch. On every trial the subject's task was to indicate with a button press the orientation of the Gabor patch. Trials were blocked by ISI duration, and each block contained 12 trials. Participants performed 5 runs of the task, with each run containing 2 blocks of trials per each of the 6 ISI conditions and one control block. Overall subjects completed 60 validly cued trials and 60 invalid trials per ISI an...
In addition to difficulty orienting to an exogenous stimulus, it is also possible that, at longer durations between cue and stimulus, when the effect of the exogenous cue has extinguished, the patient may have trouble reverting back to top-down control of attention. To test this specifically, we had our participants complete another exogenous cueing experiment, which involved an explicit reorienting cue at longer durations to allow the patient to reorient to top-down control of attention (Natale et al., ). We hoped that by explicitly instructing the patient to reorient and divide his attention between the two possible stimulus locations, he would be able to perform better at the orientation discrimination task for these longer inter-cue-stimulus duration trials. This task consisted of three trial types including: implicit exogenous cueing, exogenous cueing with explicit reorienting, and control trials (see Figure ). Implicit Exogenous Cue trials were similar to the exogenous cue trials described above such that a aatch cue with 50% validity was first presented for 50 ms, followed by a white fixation spot for either 100, 400 or 800 ms ISI duration. This was followed by a 50-ms Ga...
We confirmed that subjects fixated at the center of the screen while doing each of the three Attentional Cueing experiments by analyzing the eye-tracker data using ASL Results Plus™. Data from 4 sessions were excluded from analysis due to poor data quality. The remaining data (6 subjects for Endogenous Cueing, 5 for Exogenous Cueing, and 5 for Exogenous Cueing with Explicit Reorienting) were used to determine the percentage of fixation duration within a rectangular Area of Interest (AOI) of ±3° of visual angle around the fixation spot (Note the Gabor patch was presented at ±5.5°). The patient's eye tracking data were analyzed similarly and then compared to the average of the control group using the Single Bayesian Test.
Structural and resting state functional MRI (rsfMRI) data were acquired on a GE MR 750 3-Tesla scanner using a GE 32 channel head coil. A high-resolution structural image was acquired using a magnetization-prepared rapid-gradient-echo (MP-RAGE) T1-weighted sequence with the following parameters: time to echo [TE] = 3.42 ms; time to repetition [TR] = 7 ms; time to inversion [TI] = 425 ms; flip angle = 7°; Phase Acceleration Factor = 2; slices with 1 × 1 × 1 mm voxels). rsfMRI data were obtained using an axial echo-planar imaging (EPI) sequence ( TE = 28.1 ms; TR = 2500 ms; flip angle = 77°; Phase Acceleration Factor = 2; 44 slices, each 3 mm thick, with 2 × 2 mm in-plane voxel resolution). Two runs with 134 volumes for each run were acquired for each participant (Data for the control group were acquired as part of a larger project that is outlined in Barnes et al., ). Physiological variables relating to heart rate and respiration were recorded during scans using a pulse oximeter placed on the left index finger and a pneumatic belt positioned at the level of the diaphragm.
Machine-readable layer
[
{
"@context": "https://schema.org",
"@type": "HowTo",
"name": "A role of right middle frontal gyrus in reorienting of attention: a case study methods",
"description": "Protocol for A role of right middle frontal gyrus in reorienting of attention: a case study methods",
"step": [
{
"@type": "HowToStep",
"position": 1,
"name": "Apparatus",
"text": "Stimuli were presented on a 24″ liquid crystal display monitor, with a resolution of 1024 × 768 pixels and a refresh rate of 60 Hz, in a dimly lit room. A chin rest was used to maintain position of the participant's eyes 57 cm from the screen and to minimize head motion. Stimuli for the adaptive thresholding and Endogenous Cueing experiment were presented using MATLAB 7.4 (Mathworks, Natick, MA) and Psychophysics Toolbox (Brainard,; Pelli, ). Stimuli for Exogenous Cueing and Go/No-Go experiments were presented using Presentation (Neurobehavioral Systems, Berkeley, CA). Sustained fixation at the center of the screen was monitored using the ASL Eyetrak 6000 (Applied Science Laboratories, Bedford, MA) for 7 out of the 10 subjects for Attentional Cueing experiments. Eye tracking was not performed for the Response Inhibition experiment, since stimuli in those tasks were present..."
},
{
"@type": "HowToStep",
"position": 2,
"name": "Methods",
"text": "Figure shows the extent of the cortical resection in the patient's brain. In Talairach space, the resection spanned a region that extended from the midline of the right hemisphere ( x = 0) to a lateral location of x = 50 mm. This included the right superior frontal gyrus (SFG), right middle frontal gyrus (MFG), while almost completely sparing the right inferior frontal gyrus (IFG). Caudally the resection extended from y = 23 mm to y = ~66 mm (anterior tip of the brain). Dorsally, the resection spanned the region between z = -4 mm and z = 50 mm (superior tip of the brain). The resection removed most of Brodmann areas (BA) 9, 46, as well as the dorsal portion of BA 10, in the right hemisphere."
},
{
"@type": "HowToStep",
"position": 3,
"name": "Methods",
"text": "Coronal slices taken 6 mm apart starting posteriorly at y = 22 and showing the extent of the tumor resection in the right hemisphere. The resection encompassed right superior frontal gyrus and right middle frontal gyrus, including Brodmann areas 9, 46, and 10. Right inferior frontal gyrus was almost completely spared. In Talairach normalized space, the resection extended from x of 0 (midline) to about 50 mm, y of 23 to y of 66 mm (anterior tip of brain) and z of -4 to z of 50 mm (superior tip of brain)."
},
{
"@type": "HowToStep",
"position": 4,
"name": "Healthy controls",
"text": "Attentional cueing experiments. Ten normal volunteers (5 females) age-matched to the patient (31.8 ± 3.4; mean ± SD years) participated in the study. Subjects completed one of three attentional cueing experiments on three separate visits spanning approximately 1 week."
},
{
"@type": "HowToStep",
"position": 5,
"name": "Exogenous cueing task",
"text": "In this experiment participants were shown an exogenous stimulus (a white box) at one of two locations, to the left or right of fixation (see Figure ). This white box prior to the appearance of the Gabor patch served as the exogenous cue with 50% validity. The box was followed by a white fixation spot for a variable amount of time, i.e., inter-stimulus interval (ISI) of either 0, 50, 100, 250, 500 or 700 ms. This was then followed by the Gabor patch that appeared for 50 ms in the cued or non-cued location with 50% validity with respect to the cue. This was followed by a gray fixation spot that indicated the 1500-ms response period. Participants were instructed that the location of the white box cue was completely random and unrelated to the location of the subsequent grating patch. On every trial the subject's task was to indicate with a button press the orientation of the Gabor patch..."
},
{
"@type": "HowToStep",
"position": 6,
"name": "Exogenous cueing task with explicit reorienting",
"text": "In addition to difficulty orienting to an exogenous stimulus, it is also possible that, at longer durations between cue and stimulus, when the effect of the exogenous cue has extinguished, the patient may have trouble reverting back to top-down control of attention. To test this specifically, we had our participants complete another exogenous cueing experiment, which involved an explicit reorienting cue at longer durations to allow the patient to reorient to top-down control of attention (Natale et al., ). We hoped that by explicitly instructing the patient to reorient and divide his attention between the two possible stimulus locations, he would be able to perform better at the orientation discrimination task for these longer inter-cue-stimulus duration trials. This task consisted of three trial types including: implicit exogenous cueing, exogenous cueing with explicit reorienting, a..."
},
{
"@type": "HowToStep",
"position": 7,
"name": "Eye-tracking data analysis",
"text": "We confirmed that subjects fixated at the center of the screen while doing each of the three Attentional Cueing experiments by analyzing the eye-tracker data using ASL Results Plus™. Data from 4 sessions were excluded from analysis due to poor data quality. The remaining data (6 subjects for Endogenous Cueing, 5 for Exogenous Cueing, and 5 for Exogenous Cueing with Explicit Reorienting) were used to determine the percentage of fixation duration within a rectangular Area of Interest (AOI) of ±3° of visual angle around the fixation spot (Note the Gabor patch was presented at ±5.5°). The patient's eye tracking data were analyzed similarly and then compared to the average of the control group using the Single Bayesian Test."
},
{
"@type": "HowToStep",
"position": 8,
"name": "Resting state fMRI",
"text": "Structural and resting state functional MRI (rsfMRI) data were acquired on a GE MR 750 3-Tesla scanner using a GE 32 channel head coil. A high-resolution structural image was acquired using a magnetization-prepared rapid-gradient-echo (MP-RAGE) T1-weighted sequence with the following parameters: time to echo [TE] = 3.42 ms; time to repetition [TR] = 7 ms; time to inversion [TI] = 425 ms; flip angle = 7°; Phase Acceleration Factor = 2; slices with 1 × 1 × 1 mm voxels). rsfMRI data were obtained using an axial echo-planar imaging (EPI) sequence ( TE = 28.1 ms; TR = 2500 ms; flip angle = 77°; Phase Acceleration Factor = 2; 44 slices, each 3 mm thick, with 2 × 2 mm in-plane voxel resolution). Two runs with 134 volumes for each run were acquired for each participant (Data for the control group were acquired as part of a larger project that is outlined in Barnes et..."
}
],
"tool": [],
"supply": [],
"isBasedOn": {
"@type": "ScholarlyArticle",
"headline": "A role of right middle frontal gyrus in reorienting of attention: a case study",
"datePublished": "2015",
"author": [
{
"@type": "Person",
"name": "Shruti Japee"
},
{
"@type": "Person",
"name": "Kelsey Holiday"
},
{
"@type": "Person",
"name": "Maureen D. Satyshur"
},
{
"@type": "Person",
"name": "Ikuko Mukai"
},
{
"@type": "Person",
"name": "Leslie G. Ungerleider"
}
],
"identifier": "10.3389/fnsys.2015.00023"
}
},
{
"@context": "https://schema.org",
"@type": "BreadcrumbList",
"itemListElement": [
{
"@type": "ListItem",
"position": 1,
"name": "Experiments",
"item": "https://replicatescience.com/experiments"
},
{
"@type": "ListItem",
"position": 2,
"name": "A role of right middle frontal gyrus in reorienting of attention: a case study methods",
"item": "https://replicatescience.com/experiments/a-role-of-right-middle-frontal-gyrus-in-reorienting-of-attention-a-case-study-methods-shruti-japee-pmc4347607/a-role-of-right-middle-frontal-gyrus-in-reorienting-of-attention-a-case-study-mlph3p9v"
}
]
}
]