ENIGMA MEG data upload - Revision history

Amnamyst at 19:39, 31 January 2025

2025-01-31T19:39:44Z

← Older revision		Revision as of 15:39, 31 January 2025
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	###Fieldtrip		###Fieldtrip
	###Vendor transform (Still to be determined if this is acceptable)		###Vendor transform (Still to be determined if this is acceptable)
	##Coded subject list with age, ~~gender~~, and other demographics (TBD)		##Coded subject list with age, sex, and other demographics (TBD)
	#Information on data acquisition		#Information on data acquisition
	##EyesOpen/EyesClosed		##EyesOpen/EyesClosed

Amnamyst: Add FAQ link

2024-02-14T14:17:18Z

Add FAQ link

← Older revision		Revision as of 10:17, 14 February 2024
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	##Scanner Vendor/Model		##Scanner Vendor/Model
	##If Vertical/Horizontal EOG and ECG - provide channel numbers		##If Vertical/Horizontal EOG and ECG - provide channel numbers

			Consult the [https://megcore.nih.gov/index.php/ENIGMA_MEG_Pipeline_FAQ Pipeline FAQ] if you run into any problems.

	=Globus Website=		=Globus Website=

Jstout: /* Converting Data to BIDS */

2022-12-01T13:47:51Z

Converting Data to BIDS

← Older revision		Revision as of 09:47, 1 December 2022
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	## SPM currently does not export to BIDS - use the following scripts to make the bids files		## SPM currently does not export to BIDS - use the following scripts to make the bids files
	## https://github.com/jstout211/meg_fiducials_extract		## https://github.com/jstout211/meg_fiducials_extract
			# Biscuit
			## GUI driven BIDS conversion for KIT and Elekta data
			## https://macquarie-meg-research.github.io/Biscuit/

	=Steps prior to data upload=		=Steps prior to data upload=

Jstout at 15:52, 31 May 2022

2022-05-31T15:52:33Z

← Older revision		Revision as of 11:52, 31 May 2022
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			=Converting Data to BIDS=
			# Fieldtrip
			## data2bids.m
			# Brainstorm
			## https://neuroimage.usc.edu/brainstorm/ExportBids
			## Add fiducials to MRI json: https://github.com/jstout211/meg_fiducials_extract
			# SPM
			## SPM currently does not export to BIDS - use the following scripts to make the bids files
			## https://github.com/jstout211/meg_fiducials_extract

	=Steps prior to data upload=		=Steps prior to data upload=
	(if data is already anonymized+bids format skip this section) <br>		(if data is already anonymized+bids format skip this section) <br>

Jstout at 15:14, 23 May 2022

2022-05-23T15:14:00Z

← Older revision		Revision as of 11:14, 23 May 2022
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	[[File:GlobusUploadConfirmation.png \|900px \| Alt text]]		[[File:GlobusUploadConfirmation.png \|900px \| Alt text]]
	<br><br>		<br><br>


			==Admin - Globus Endpoint Creation (Ignore)==
			Setup Endpoint [https://megcore.nih.gov/index.php?title=Administer_globus_endpoint Globus]

Jstout: /* Steps prior to data upload */

2021-03-22T20:15:55Z

Steps prior to data upload

← Older revision		Revision as of 16:15, 22 March 2021
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	###Vendor transform (Still to be determined if this is acceptable)		###Vendor transform (Still to be determined if this is acceptable)
	##Coded subject list with age, gender, and other demographics (TBD)		##Coded subject list with age, gender, and other demographics (TBD)
			#Information on data acquisition
			##EyesOpen/EyesClosed
			##VerticalAcquisition/SupineAcquisition
			##Scanner Vendor/Model
			##If Vertical/Horizontal EOG and ECG - provide channel numbers

	=Globus Website=		=Globus Website=

Amnamyst: /* Data upload process */

2021-02-26T17:12:38Z

Data upload process

← Older revision		Revision as of 13:12, 26 February 2021
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	<br><br>		<br><br>

	*'''Start Globus Connect Personal on your computer to interact with local files/folders.		*'''Start Globus Connect Personal on your computer to interact with local files/folders.'''
	~~<br>~~If no collection available - see next section to create endpoint'''		''If no collection available - see next section to create endpoint.''
	<br>		<br>
	[[File:GlobusConnectLocalContent.png \|900px \| Alt text]]		[[File:GlobusConnectLocalContent.png \|900px \| Alt text]]

Amnamyst: /* Data upload process */

2021-02-26T17:06:33Z

Data upload process

← Older revision		Revision as of 13:06, 26 February 2021
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	=Data upload process=		=Data upload process=
	'''~~---~~DATA MUST BE ANONYMIZED BEFORE UPLOAD!~~---~~'''		<big>'''* DATA MUST BE ANONYMIZED BEFORE UPLOAD! *'''</big>
	<br><br>		<br><br>
	'''*Log into the Globus website to view main menu'''		*'''Log into the Globus website to view main menu'''
	<br>		<br>
	[[File:GlobusMainMenu.png\| 900px \| Alt text]]		[[File:GlobusMainMenu.png\| 900px \| Alt text]]
	<br><br>		<br><br>

	'''*Find remote endpoint - Click the search field'''		*'''Find remote endpoint - Click the search field'''
	<br>		<br>
	[[File:GlobusSearch.png\| 900px \| Alt text]]		[[File:GlobusSearch.png\| 900px \| Alt text]]
	<br><br>		<br><br>

	'''*Select Remote Endpoint provided over email - Go to the "Your Collections" or "Shared With You" tab'''		*'''Select Remote Endpoint provided over email - Go to the "Your Collections" or "Shared With You" tab'''
	<br>		<br>
	[[File:GlobusSelectEndpoint.png \| 900px \| Alt text]]		[[File:GlobusSelectEndpoint.png \| 900px \| Alt text]]
	<br><br>		<br><br>

	'''*Connected to Remote Endpoint - View Contents and select folder (It is possible that the folder is empty) '''		*'''Connected to Remote Endpoint - View Contents and select folder (It is possible that the folder is empty) '''
	<br>		<br>
	[[File:GlobusConnectRemote.png \| 900px \| Alt text]]		[[File:GlobusConnectRemote.png \| 900px \| Alt text]]
	<br><br>		<br><br>

	'''*Start Globus Connect Personal on your computer to interact with local files/folders.		*'''Start Globus Connect Personal on your computer to interact with local files/folders.
	<br>If no collection available - see next section to create endpoint'''		<br>If no collection available - see next section to create endpoint'''
	<br>		<br>
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	<br><br>		<br><br>

	'''*Create a local endpoint (on your computer)'''		*'''Create a local endpoint (on your computer)'''
	<br>		<br>
	[[File:GlobusCreateLocalEndpoint.png \|900px \| Alt text]]		[[File:GlobusCreateLocalEndpoint.png \|900px \| Alt text]]
	<br><br>		<br><br>

	'''*Navigate Local Path. Select Data. Hit Start to initiate upload'''		*'''Navigate Local Path. Select Data. Hit Start to initiate upload'''
	<br>		<br>
	[[File:GlobusLocalDataSearchForUpload.png \|900px \| Alt text]]		[[File:GlobusLocalDataSearchForUpload.png \|900px \| Alt text]]
	<br><br>		<br><br>

	'''*Visualize Ongoing Activity '''		*'''Visualize Ongoing Activity '''
	<br>		<br>
	[[File:GlobusVisualizeOngoingActivity.png \|900px \| Alt text]]		[[File:GlobusVisualizeOngoingActivity.png \|900px \| Alt text]]
	<br><br>		<br><br>

	'''*After completion: Globus upload details and email of successful transfer'''		*'''After completion: Globus upload details and email of successful transfer'''
	<br>		<br>
	[[File:GlobusUploadConfirmation.png \|900px \| Alt text]]		[[File:GlobusUploadConfirmation.png \|900px \| Alt text]]

Jstout: /* Steps prior to data upload */

2021-02-26T02:59:22Z

Steps prior to data upload

← Older revision		Revision as of 22:59, 25 February 2021
Line 20:		Line 20:
	###Fieldtrip		###Fieldtrip
	###Vendor transform (Still to be determined if this is acceptable)		###Vendor transform (Still to be determined if this is acceptable)
	##~~Subject~~ list with age, gender, and other demographics (TBD)		##Coded subject list with age, gender, and other demographics (TBD)

	=Globus Website=		=Globus Website=

Jstout: /* Steps prior to data upload */

2021-02-26T02:31:06Z

Steps prior to data upload

← Older revision		Revision as of 22:31, 25 February 2021
Line 1:		Line 1:
	=Steps prior to data upload=		=Steps prior to data upload=
			(if data is already anonymized+bids format skip this section) <br>
	#Anonymize MEG data		#Anonymize MEG data
	#Anonymize and deface MRI (options below)		#Anonymize and deface MRI (options below)