experiment-design

Name: experiment-design
Author: neuromechanist

37stars7forks

How to install experiment-design?

neuromechanist/research-skills/experiment-design

$npx -y skills add neuromechanist/research-skills --skill experiment-design

Installs into the current project.

Summary

Use this skill for \"design experiment\", \"create PsychoPy experiment\", \"stimulus presentation\", \"experiment protocol\", \"timing validation\", \"trial structure\", \"block design\", \"event-related design\", \"PsychoPy builder\", \"create stimuli\", \"LSL markers\", \"Lab S

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SKILL.md

1	# Experiment Design
2
3	Design and implement neuroscience experiments with PsychoPy, including stimulus presentation, timing validation, event markers, and Lab Streaming Layer (LSL) integration.
4
5	## When to Use
6
7	- Designing a new behavioral or neuroimaging experiment
8	- Creating PsychoPy scripts for stimulus presentation
9	- Setting up event markers via LSL or parallel port
10	- Validating timing accuracy
11	- Converting an experiment protocol to code
12
13	## Experiment Design Principles
14
15	### Trial Structure
16
17	Every trial consists of:
18
19	```
20	[Fixation] -> [Stimulus] -> [Response Window] -> [Inter-trial Interval]
21	\| \| \| \|
22	marker marker marker marker
23	```
24
25	### Design Types
26
27	\| Design \| Best For \| Example \|
28	\|--------\|----------\|---------\|
29	\| Block \| fMRI, sustained attention \| 30s blocks of condition A, B \|
30	\| Event-related \| ERP/EEG, rapid events \| Randomized single trials \|
31	\| Mixed \| Both sustained and transient \| Blocks with jittered events \|
32	\| Resting state \| Baseline/connectivity \| Eyes open/closed periods \|
33
34	### Timing Considerations
35
36	- Frame-based timing (preferred): Specify durations in frames, not seconds
37	- Monitor refresh rate: 60 Hz = 16.67 ms/frame; 120 Hz = 8.33 ms/frame
38	- Stimulus onset: Sync to vertical blank for precise timing
39	- Jitter: Add random ITI variation for event-related designs (avoid expectation effects)
40	- Minimum stimulus duration: 1 frame (16.67 ms at 60 Hz)
41
42	## PsychoPy Experiment Template
43
44	### Basic Structure
45
46	```python
47	from psychopy import visual, core, event, data, gui
48	import numpy as np
49
50	# Experiment parameters
51	exp_info = {
52	"participant": "",
53	"session": "01",
54	"task": "experiment_name",
55	}
56
57	# GUI dialog
58	dlg = gui.DlgFromDict(exp_info, title="Experiment")
59	if not dlg.OK:
60	core.quit()
61
62	# Window setup
63	win = visual.Window(
64	size=[1920, 1080],
65	fullscr=True,
66	monitor="testMonitor",
67	units="deg",
68	color=[0, 0, 0],
69	)
70
71	# Stimuli
72	fixation = visual.TextStim(win, text="+", height=2)
73	stimulus = visual.ImageStim(win, image=None, size=[10, 10])
74	feedback = visual.TextStim(win, text="", height=1.5)
75
76	# Trial handler
77	conditions = data.importConditions("conditions.xlsx")
78	trials = data.TrialHandler(
79	conditions,
80	nReps=1,
81	method="random",
82	)
83
84	# Clock
85	clock = core.Clock()
86
87	# Main experiment loop
88	for trial in trials:
89	# Fixation
90	fixation.draw()
91	win.flip()
92	core.wait(0.5) # 500 ms fixation
93
94	# Stimulus
95	stimulus.image = trial["stimulus_file"]
96	stimulus.draw()
97	win.flip()
98	# Send marker here
99
100	# Response
101	clock.reset()
102	keys = event.waitKeys(
103	maxWait=2.0,
104	keyList=["left", "right", "escape"],
105	timeStamped=clock,
106	)
107
108	if keys:
109	if keys[0][0] == "escape":
110	core.quit()
111	trials.addData("response", keys[0][0])
112	trials.addData("rt", keys[0][1])
113
114	# ITI (jittered)
115	iti = np.random.uniform(0.8, 1.2)
116	core.wait(iti)
117
118	# Save data
119	import os
120	os.makedirs("data", exist_ok=True)
121	trials.saveAsWideText(f"data/sub-{exp_info['participant']}_task-{exp_info['task']}.csv")
122	win.close()
123	core.quit()
124	```
125
126	### Conditions File Format
127
128	```
129	# conditions.xlsx or conditions.csv
130	stimulus_file,condition,correct_response
131	stimuli/face01.png,face,left
132	stimuli/house01.png,house,right
133	stimuli/face02.png,face,left
134	```
135
136	## Lab Streaming Layer (LSL) Integration
137
138	### Sending Markers
139
140	```python
141	from pylsl import StreamInfo, StreamOutlet
142
143	# Create marker stream
144	info = StreamInfo(
145	name="ExperimentMarkers",
146	type="Markers",
147	channel_count=1,
148	nominal_srate=0, # irregular rate
149	channel_format="string",
150	source_id="psychopy_markers",
151	)
152	outlet = StreamOutlet(info)
153
154	# Send marker at stimulus onset
155	stimulus.draw()
156	win.flip()
157	outlet.push_sample(["stimulus_onset"]) # Send immediately after flip
158	```
159
160	### Common Marker Scheme
161
162	\| Marker \| Code \| Description \|
163	\|--------\|------\|-------------\|
164	\| stimulus_onset \| S1-S99 \| Stimulus presentation \|
165	\| response \| R1-R4 \| Participant response \|
166	\| feedback \| F1-F2 \| Correct/incorrect feedback \|
167	\| block_start \| B1-B10 \| Block onset \|
168	\| block_end \| BE \| Block offset \|
169	\| trial_start \| T \| Trial onset \|
170	\| experiment_start \| EXP_START \| First trial \|
171	\| experiment_end \| EXP_END \| Last trial \|
172
173	### HED Annotation for Markers
174
175	Annotate events with Hierarchical Event Descriptors (HED) for standardized event description:
176
177	```tsv
178	onset duration trial_type value HED
179	0.0 0.0 stimulus S1 Sensory-event, Visual-presenta

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Type

experiment-design

37stars7forks

View on GitHub

How to install experiment-design?

neuromechanist/research-skills/experiment-design

$npx -y skills add neuromechanist/research-skills --skill experiment-design

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Experiment Design
2
3	Design and implement neuroscience experiments with PsychoPy, including stimulus presentation, timing validation, event markers, and Lab Streaming Layer (LSL) integration.
4
5	## When to Use
6
7	- Designing a new behavioral or neuroimaging experiment
8	- Creating PsychoPy scripts for stimulus presentation
9	- Setting up event markers via LSL or parallel port
10	- Validating timing accuracy
11	- Converting an experiment protocol to code
12
13	## Experiment Design Principles
14
15	### Trial Structure
16
17	Every trial consists of:
18
19	```
20	[Fixation] -> [Stimulus] -> [Response Window] -> [Inter-trial Interval]
21	\| \| \| \|
22	marker marker marker marker
23	```
24
25	### Design Types
26
27	\| Design \| Best For \| Example \|
28	\|--------\|----------\|---------\|
29	\| Block \| fMRI, sustained attention \| 30s blocks of condition A, B \|
30	\| Event-related \| ERP/EEG, rapid events \| Randomized single trials \|
31	\| Mixed \| Both sustained and transient \| Blocks with jittered events \|
32	\| Resting state \| Baseline/connectivity \| Eyes open/closed periods \|
33
34	### Timing Considerations
35
36	- Frame-based timing (preferred): Specify durations in frames, not seconds
37	- Monitor refresh rate: 60 Hz = 16.67 ms/frame; 120 Hz = 8.33 ms/frame
38	- Stimulus onset: Sync to vertical blank for precise timing
39	- Jitter: Add random ITI variation for event-related designs (avoid expectation effects)
40	- Minimum stimulus duration: 1 frame (16.67 ms at 60 Hz)
41
42	## PsychoPy Experiment Template
43
44	### Basic Structure
45
46	```python
47	from psychopy import visual, core, event, data, gui
48	import numpy as np
49
50	# Experiment parameters
51	exp_info = {
52	"participant": "",
53	"session": "01",
54	"task": "experiment_name",
55	}
56
57	# GUI dialog
58	dlg = gui.DlgFromDict(exp_info, title="Experiment")
59	if not dlg.OK:
60	core.quit()
61
62	# Window setup
63	win = visual.Window(
64	size=[1920, 1080],
65	fullscr=True,
66	monitor="testMonitor",
67	units="deg",
68	color=[0, 0, 0],
69	)
70
71	# Stimuli
72	fixation = visual.TextStim(win, text="+", height=2)
73	stimulus = visual.ImageStim(win, image=None, size=[10, 10])
74	feedback = visual.TextStim(win, text="", height=1.5)
75
76	# Trial handler
77	conditions = data.importConditions("conditions.xlsx")
78	trials = data.TrialHandler(
79	conditions,
80	nReps=1,
81	method="random",
82	)
83
84	# Clock
85	clock = core.Clock()
86
87	# Main experiment loop
88	for trial in trials:
89	# Fixation
90	fixation.draw()
91	win.flip()
92	core.wait(0.5) # 500 ms fixation
93
94	# Stimulus
95	stimulus.image = trial["stimulus_file"]
96	stimulus.draw()
97	win.flip()
98	# Send marker here
99
100	# Response
101	clock.reset()
102	keys = event.waitKeys(
103	maxWait=2.0,
104	keyList=["left", "right", "escape"],
105	timeStamped=clock,
106	)
107
108	if keys:
109	if keys[0][0] == "escape":
110	core.quit()
111	trials.addData("response", keys[0][0])
112	trials.addData("rt", keys[0][1])
113
114	# ITI (jittered)
115	iti = np.random.uniform(0.8, 1.2)
116	core.wait(iti)
117
118	# Save data
119	import os
120	os.makedirs("data", exist_ok=True)
121	trials.saveAsWideText(f"data/sub-{exp_info['participant']}_task-{exp_info['task']}.csv")
122	win.close()
123	core.quit()
124	```
125
126	### Conditions File Format
127
128	```
129	# conditions.xlsx or conditions.csv
130	stimulus_file,condition,correct_response
131	stimuli/face01.png,face,left
132	stimuli/house01.png,house,right
133	stimuli/face02.png,face,left
134	```
135
136	## Lab Streaming Layer (LSL) Integration
137
138	### Sending Markers
139
140	```python
141	from pylsl import StreamInfo, StreamOutlet
142
143	# Create marker stream
144	info = StreamInfo(
145	name="ExperimentMarkers",
146	type="Markers",
147	channel_count=1,
148	nominal_srate=0, # irregular rate
149	channel_format="string",
150	source_id="psychopy_markers",
151	)
152	outlet = StreamOutlet(info)
153
154	# Send marker at stimulus onset
155	stimulus.draw()
156	win.flip()
157	outlet.push_sample(["stimulus_onset"]) # Send immediately after flip
158	```
159
160	### Common Marker Scheme
161
162	\| Marker \| Code \| Description \|
163	\|--------\|------\|-------------\|
164	\| stimulus_onset \| S1-S99 \| Stimulus presentation \|
165	\| response \| R1-R4 \| Participant response \|
166	\| feedback \| F1-F2 \| Correct/incorrect feedback \|
167	\| block_start \| B1-B10 \| Block onset \|
168	\| block_end \| BE \| Block offset \|
169	\| trial_start \| T \| Trial onset \|
170	\| experiment_start \| EXP_START \| First trial \|
171	\| experiment_end \| EXP_END \| Last trial \|
172
173	### HED Annotation for Markers
174
175	Annotate events with Hierarchical Event Descriptors (HED) for standardized event description:
176
177	```tsv
178	onset duration trial_type value HED
179	0.0 0.0 stimulus S1 Sensory-event, Visual-presenta

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6 picks

Type