Healthy Volunteer Protocol Upload Process - Revision history

Jstout: /* Processing steps in process_hv_data.py */

2020-05-29T19:16:13Z

Processing steps in process_hv_data.py

← Older revision		Revision as of 15:16, 29 May 2020
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	Remove history files and replace paths/dates/names in text files		Remove history files and replace paths/dates/names in text files

			==Add data and logfile paths to bashrc==
			in ~/.basrhc
			export hv_meg_path=/$PATH
			export hv_logfile_path=/$PATHlogfile

	==Processing steps in process_hv_data.py==		==Processing steps in process_hv_data.py==

Jstout: /* Task Specific Processing */

2020-05-27T20:33:34Z

Task Specific Processing

← Older revision		Revision as of 16:33, 27 May 2020
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	==Task Specific Processing==		==Task Specific Processing==
	All task processing scripts have a commandline parsing component that can be called independently. The typical format is below.		All task processing scripts have a commandline parsing component that can be called independently. The typical format is below. If print_stats_only is flagged, then the results will not be output to the marker file. This can be useful if the QA fails or to check results after a change in the stimulus setup.

	[[File:Process_help.png \| 700px]]		[[File:Process_help.png \| 700px]]

Jstout: /* Task Specific Processing */

2020-05-27T19:54:43Z

Task Specific Processing

← Older revision		Revision as of 15:54, 27 May 2020
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	==Task Specific Processing==		==Task Specific Processing==
	All task processing scripts have a commandline parsing component that can be called independently. The typical format is below.		All task processing scripts have a commandline parsing component that can be called independently. The typical format is below.

			[[File:Process_help.png \| 700px]]

	===Oddball Task===		===Oddball Task===

Jstout: /* Task Specific Processing */

2020-05-27T19:41:15Z

Task Specific Processing

← Older revision		Revision as of 15:41, 27 May 2020
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	==Task Specific Processing==		==Task Specific Processing==
			All task processing scripts have a commandline parsing component that can be called independently. The typical format is below.

	===Oddball Task===		===Oddball Task===
	Description: 3 sound stimuli presented to the participant. The participant attends to the "standard" tone stimuli (210 epochs) and is required to respond to the "target" tone stimuli (45 epochs) that are intermixed with the standard tone. Additionally a broadband noise stimuli is presented as a "distractor" stimuli (45 epochs).		Description: 3 sound stimuli presented to the participant. The participant attends to the "standard" tone stimuli (210 epochs) and is required to respond to the "target" tone stimuli (45 epochs) that are intermixed with the standard tone. Additionally a broadband noise stimuli is presented as a "distractor" stimuli (45 epochs).

Jstout: /* Processing steps in process_hv_data.py */

2020-05-27T17:20:13Z

Processing steps in process_hv_data.py

← Older revision		Revision as of 13:20, 27 May 2020
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	Process Tasks and assert ouputs match expected:		Process Tasks and assert ouputs match expected:
	~~airpuff_processing~~.py		process_airpuff.py
	~~oddball_processing~~.py		process_oddball.py
	~~hariri_processing~~.py		process_hariri.py
			process_sternberg.py
	sternberg_processing.py
	~~gonogo_processing~~.py		process_gonogo.py

	Calculate the noise level		Calculate the noise level
	Scrub path info and history text files from the datasets to remove date and identifiers		Scrub path info and history text files from the datasets to remove date and identifiers


	==General Task Analysis Processing==		==General Task Analysis Processing==

Jstout: /* General Task Analysis Processing */

2020-05-27T17:18:13Z

General Task Analysis Processing

← Older revision		Revision as of 13:18, 27 May 2020
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	==General Task Analysis Processing==		==General Task Analysis Processing==
	===Invert Trigger===		===Invert Trigger===
	During some tasks the trigger randomly inverts. ~~For~~ ~~triggers a~~ histogram is ~~created~~ ~~with~~ the top two bins ~~representing~~ the ON and OFF state of the stimuli. The expectation is that the OFF state should represent more time during the task than the ON state, if not the trigger is inverted prior to analysis.		During some tasks the trigger randomly inverts. A 10-bin histogram is calculated for the analog trigger channels. The top two bins by count represent the ON and OFF state of the stimuli. The expectation is that the OFF state should represent more time during the task than the ON state, if not the trigger is inverted prior to analysis.

	===Threshold Detection===		===Threshold Detection===
	Amplitude detection based on normalizing analog signal between 0 and 1 and derivative threshold. Temporary filters may be applied to the data during this operation.		Amplitude detection based on normalizing analog signal between 0 and 1. The threshold is then applied to the normalized signal and an optional derivative threshold. Temporary filters may be applied to the data during this operation.

	===Merge Logfile===		===Merge Logfile===
	For psychoPy tasks (Sternberg, Hariri, oddball), the text logfile is imported. The first few timepoints representing instruction screens are removed from the file and the rest are added to the dataframe.		For psychoPy tasks (Sternberg, Hariri, oddball), the text logfile (.log) is imported. The first few timepoints representing instruction screens are removed from the file and the rest are added to the dataframe.

	===Coding Analog stimuli with Parallel port Values===		===Coding Analog stimuli with Parallel port Values===
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	===Reset Timing to Optical Trigger===		===Reset Timing to Optical Trigger===
	Due to projector frame buffering there can be timing jitter in the presentation of visual stimuli to the subject. The ~~stimuli~~ computer sends a parallel port trigger to the acquisition computer and the stimuli to the projector. The visual tasks have been designed to activate the upper right corner with a specific bit value The projector - Propix (model ????) has an output BNC signal that triggers when the		Due to projector frame buffering there can be timing jitter in the presentation of visual stimuli to the subject. The stimulus computer sends a parallel port trigger to the acquisition computer and the stimuli to the projector. The visual tasks have been designed to activate the upper right corner with a specific bit value The projector - Propix (model ????) has an output BNC signal that triggers when the top right pixel is set to the value 255 (??). This optical trigger is coded on channel UADC016.

	===Response Coding===		===Response Coding===
			The correct response is calculated from either the parrallel port trigger or the logfile information depending on the task. The expected responses are judged against the response to determine if a response_hit, response_miss, response_false_alarm, response_correct_rejection. Some tasks require a response for every stimuli (eg hariri_hammer), while others require responses
	The correct response is calculated....


	==Task Specific Processing==		==Task Specific Processing==

Jstout: /* BIDS format / OpenNeuro */

2020-05-27T17:00:04Z

BIDS format / OpenNeuro

← Older revision		Revision as of 13:00, 27 May 2020
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	==BIDS format / OpenNeuro==		==BIDS format / OpenNeuro==
	All data is be converted to BIDS format and uploaded to OpenNeuro as an open access dataset.		All data is converted to BIDS format and uploaded to OpenNeuro as an open access dataset.
	Data triggers are cleaned using several routines listed below. These have been used to realign stimulus triggers to optical onset of the projector. Datasets that have logfiles have been merged		Data triggers are cleaned using several routines listed below. These have been used to realign stimulus triggers to optical onset of the projector. Datasets that have logfiles have been merged
	with the trigger data to label triggers and responses.		with the trigger data to label triggers and responses.


	==Processing on Biowulf==		==Processing on Biowulf==

Jstout at 18:28, 13 May 2020

2020-05-13T18:28:55Z

← Older revision		Revision as of 14:28, 13 May 2020
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	Files have been compiled into a folder hv_proc		Files have been compiled into a folder hv_proc
	This contains script interfaces into the megblocks package		This contains script interfaces into the megblocks package

			=Data Quality Assurance and PreUpload=
			Verify that all tasks have the appropriate number of triggers
			hv_proc/utilities/marker_quality_assurance.py -data_folder $DATA

Jstout: /* General Task Analysis Processing */

2020-05-12T20:26:12Z

General Task Analysis Processing

← Older revision		Revision as of 16:26, 12 May 2020
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			==Task Specific Processing==

	===Oddball Task===		===Oddball Task===
	Description: 3 sound stimuli presented to the participant. The participant attends to the "standard" tone stimuli (210 epochs) and is required to respond to the "target" tone stimuli (45 epochs) that are intermixed with the standard tone. Additionally a broadband noise stimuli is presented as a "distractor" stimuli (45 epochs).		Description: 3 sound stimuli presented to the participant. The participant attends to the "standard" tone stimuli (210 epochs) and is required to respond to the "target" tone stimuli (45 epochs) that are intermixed with the standard tone. Additionally a broadband noise stimuli is presented as a "distractor" stimuli (45 epochs).

Jstout: /* General Task Analysis Processing */

2020-05-12T20:24:40Z

General Task Analysis Processing

← Older revision		Revision as of 16:24, 12 May 2020
Line 70:		Line 70:
	===Invert Trigger===		===Invert Trigger===
	During some tasks the trigger randomly inverts. For triggers a histogram is created with the top two bins representing the ON and OFF state of the stimuli. The expectation is that the OFF state should represent more time during the task than the ON state, if not the trigger is inverted prior to analysis.		During some tasks the trigger randomly inverts. For triggers a histogram is created with the top two bins representing the ON and OFF state of the stimuli. The expectation is that the OFF state should represent more time during the task than the ON state, if not the trigger is inverted prior to analysis.

			===Threshold Detection===
			Amplitude detection based on normalizing analog signal between 0 and 1 and derivative threshold. Temporary filters may be applied to the data during this operation.

	===Merge Logfile===		===Merge Logfile===
Line 75:		Line 78:

	===Coding Analog stimuli with Parallel port Values===		===Coding Analog stimuli with Parallel port Values===
			Analog triggers are generally converted to single states (ON/OFF), the parallel port can be used to code the output values

	===Reset Timing to Optical Trigger===		===Reset Timing to Optical Trigger===
	Due to projector frame buffering there can be timing jitter in the presentation of visual stimuli to the subject. The stimuli computer sends a parallel port trigger to the acquisition computer and the stimuli to the projector. The visual tasks have been designed to activate the upper right corner with a specific bit value The projector - Propix (model ????) has an output BNC signal that triggers when the		Due to projector frame buffering there can be timing jitter in the presentation of visual stimuli to the subject. The stimuli computer sends a parallel port trigger to the acquisition computer and the stimuli to the projector. The visual tasks have been designed to activate the upper right corner with a specific bit value The projector - Propix (model ????) has an output BNC signal that triggers when the

			===Response Coding===
			The correct response is calculated....