Data Access - Revision history

imported>Lmperry at 23:16, 4 December 2019

2019-12-04T23:16:47Z

← Older revision		Revision as of 23:16, 4 December 2019
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	The CNI uses [https://flywheel.io Flywheel] for data management and access. Please see the [[ Flywheel \| Flywheel ]] page for more information regarding data access.		The CNI uses [https://flywheel.io Flywheel] for data management and access. Please see the [[ Flywheel \| Flywheel ]] page for more information regarding data access via Flywheel.

	= Data Sharing =		= Data Sharing =

imported>Lmperry at 23:16, 4 December 2019

2019-12-04T23:16:26Z

← Older revision		Revision as of 23:16, 4 December 2019
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	The CNI uses [ https://flywheel.io Flywheel] for data management and access. Please see the [[ Flywheel \| Flywheel ]] page for more information regarding data access.		The CNI uses [https://flywheel.io Flywheel] for data management and access. Please see the [[ Flywheel \| Flywheel ]] page for more information regarding data access.

	= Data Sharing =		= Data Sharing =
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	# Find the data to be shared and note the experiment name, subject code, and session numbers.		# Find the data to be shared and note the experiment name, subject code, and session numbers.
	# Contact the principal investigator and officially ask for the data to be shared. ''Contact should be between PIs.''		# Contact the principal investigator and officially ask for the data to be shared. ''Contact should be between PIs.''
	# Once permission is granted you can log into [~~http~~://cni.~~stanford~~.~~edu/nimsgears NIMS~~] and download the data.		# Once permission is granted you can log into [https://cni.flywheel.io Flywheel] and download the data.
	</ol>		</ol>
	'''The persons responsible for the data (PI or Lab Manager):'''		'''The persons responsible for the data (PI or Lab Manager):'''
	<ol>		<ol>
	# Assure that the IRB protocol under which the data were collected allows for data sharing.		# Assure that the IRB protocol under which the data were collected allows for data sharing.
	# Log into [~~http~~://cni.~~stanford~~.~~edu/nimsgears NIMS~~]		# Log into [https://cni.flywheel.io Flywheel]
	~~# Navigate to the 'Manage Experiments' page~~
	~~# Find the experiment that will be shared~~
	~~# Drag the sunetid of the person with which you will be sharing the data over the experiment name and choose the permissions level you wish to grant.~~
	</ol>		</ol>

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	<li> Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.</li>		<li> Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.</li>
	<li> After they have confirmed that they have granted you permission navigate to the ~~NIMS~~ interface, find the experiment with the data and ~~drag it to the~~ 'Download' ~~icon.~~ </li>		<li> After they have confirmed that they have granted you permission navigate to the Flywheel interface, find the experiment with the data and 'Download' those data </li>
	</ol>		</ol>

imported>Lmperry at 23:13, 4 December 2019

2019-12-04T23:13:51Z

← Older revision		Revision as of 23:13, 4 December 2019
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	The CNI ~~has developed an integrated neurobiological image management system (NIMS) to facilitate the stewardship of all data collected at the CNI. NIMS is currently under active development.~~ [https://~~cni.stanford.edu/nims/ NIMS 1~~.0]~~) is currently deployed~~ and ~~used by all CNI users to securely~~ access ~~their scan data~~. ~~This system is useful for organizing and archiving the data that users collect here. NIMS 2.0 is currently under active development; check the status on [https://github.com/cni/nims/ github page].~~		The CNI uses [ https://flywheel.io Flywheel] for data management and access. Please see the [[ Flywheel \| Flywheel ]] page for more information regarding data access.

	~~For more information on our NIMS software development efforts,~~ see the [[~~NIMS~~ \| ~~CNI Software Development page~~]].

	~~= The Reapers: Automatic~~ data ~~transfer to nims =~~

	A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. The ''reapers'' are ever-running processes that reap images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''cnifs''') that's accessible via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. In '''nims''', the data are organized by the group name, an experiment name (both set at scan-time in the '''PatientID''' field), and exam date. Dicoms are archived in tar-gz files (one per acquisition) and are also converted to a NIfTI file (also one per acquisition). P-files are copied into this same folder, and P-files from our custom PSDs (e.g., spiral and SMS-EPI) are reconstructed and the resulting images saved in a NIfTI. Physio data, if recorded, are saved on nims as well.

	~~=== Data Organization ===~~

	~~Data acquired during a session can be automatically organized for you with a custom Subject Code by entering a "'sorting string'" into the '''PatientID''' field on the exam setup page.~~

	~~The sorting string works as follows:~~

	~~<subject_code>@<group_name>/<experiment_name>~~
	~~<br>~~
	~~For example, the following string in the '''PatientID''' field would organize the given session into the "colorblind" experiment within the Wandell group, with the subject code of "ColorBlind_s83":~~
	~~ColorBlind_s83@wandell/colorblind~~
	~~<br>~~
	~~'''Please note the following:'''~~

	* While ''<subject_code>'' and ''<experiment_name>'' will be created at scan time, the ''<group_name>'' must match the Principal Investigator's SUNetID (e.g. ''wandell'').
	* ''<subject_code>'' is not required and will default to the exam number.
	* If the sorting string is incorrect and can't be matched to a PI it will be placed into the ''unknown'' group and a CNI admin will need to help you retrieve and organize it correctly.

	= Data Sharing =		= Data Sharing =

imported>Lmperry: /* Data Organization */

2016-10-24T22:17:00Z

Data Organization

← Older revision		Revision as of 22:17, 24 October 2016
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	=== Data Organization ===		=== Data Organization ===

	Data acquired during a session can be automatically organized for you with a custom Subject Code by entering a "sorting string" into the '''PatientID''' field on the exam setup page.		Data acquired during a session can be automatically organized for you with a custom Subject Code by entering a "'sorting string'" into the '''PatientID''' field on the exam setup page.

	The sorting string works as follows:		The sorting string works as follows:
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	<subject_code>@<group_name>/<experiment_name>		<subject_code>@<group_name>/<experiment_name>
	<br>		<br>
	For example, the following string would organize the given session into the ''colorblind' experiment within the Wandell group, with the subject code of ''ColorBlind_s83'':		For example, the following string in the '''PatientID''' field would organize the given session into the "colorblind" experiment within the Wandell group, with the subject code of "ColorBlind_s83":
	ColorBlind_s83@wandell/colorblind		ColorBlind_s83@wandell/colorblind
	<br>		<br>
	'''Please note the following:'''		'''Please note the following:'''
	~~<i>~~
	* While <subject_code> and <experiment_name> will be created at scan time, the <group_name> must match the Principal Investigator's SUNetID (e.g. ''wandell'').		* While ''<subject_code>'' and ''<experiment_name>'' will be created at scan time, the ''<group_name>'' must match the Principal Investigator's SUNetID (e.g. ''wandell'').
	* <subject_code> is not required and will default to the exam number.		* ''<subject_code>'' is not required and will default to the exam number.
	* If the sorting string is incorrect and can't be matched to a PI it will be placed into the ''unknown'' group and a CNI admin will need to help you retrieve and organize it correctly.		* If the sorting string is incorrect and can't be matched to a PI it will be placed into the ''unknown'' group and a CNI admin will need to help you retrieve and organize it correctly.
	~~</i>~~

	= Data Sharing =		= Data Sharing =

imported>Lmperry: /* Data Organization */

2016-10-24T22:14:53Z

Data Organization

← Older revision		Revision as of 22:14, 24 October 2016
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	<br>		<br>
	'''Please note the following:'''		'''Please note the following:'''
	<em>		<i>
	* While <subject_code> and <experiment_name> will be created as scan time, the ~~group name~~ must match the Principal ~~Investigators~~ SUNetID (e.g. ''wandell'').		* While <subject_code> and <experiment_name> will be created at scan time, the <group_name> must match the Principal Investigator's SUNetID (e.g. ''wandell'').
	* <subject_code> is not required and will default to the exam number.		* <subject_code> is not required and will default to the exam number.
	* If the sorting string is incorrect and can't be matched to a PI it will be placed into the ''unknown'' group and a CNI admin will need to help you retrieve and organize it correctly.		* If the sorting string is incorrect and can't be matched to a PI it will be placed into the ''unknown'' group and a CNI admin will need to help you retrieve and organize it correctly.
	</em>		</i>

	= Data Sharing =		= Data Sharing =
	This section describes the way in which data can be shared among researchers.		This section describes the way in which data can be shared among researchers.

imported>Lmperry at 22:14, 24 October 2016

2016-10-24T22:14:02Z

@@ Line 7: / Line 7: @@
 A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. The ''reapers'' are ever-running processes that reap images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''cnifs''') that's accessible via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. In '''nims''', the data are organized by the group name, an experiment name (both set at scan-time in the '''PatientID''' field), and exam date. Dicoms are archived in tar-gz files (one per acquisition) and are also converted to a NIfTI file (also one per acquisition). P-files are copied into this same folder, and P-files from our custom PSDs (e.g., spiral and SMS-EPI) are reconstructed and the resulting images saved in a NIfTI. Physio data, if recorded, are saved on nims as well.
 = Data Sharing =
 This section describes the way in which data can be shared among researchers.

imported>Bobd at 17:31, 5 March 2014

2014-03-05T17:31:39Z

← Older revision		Revision as of 17:31, 5 March 2014
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	For more information on our NIMS software development efforts, see the [[NIMS \| CNI Software Development page]].		For more information on our NIMS software development efforts, see the [[NIMS \| CNI Software Development page]].

	= ~~mrReaper~~: Automatic data transfer to nims =		= The Reapers: Automatic data transfer to nims =

	A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. The ''~~reaper~~'' ~~is an~~ ever-running processes that ~~manage~~ images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''cnifs''') that's accessible via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. In '''nims''', the data are organized by the group name, an experiment name (both set at scan-time in the '''PatientID''' field), and exam date. Dicoms are archived in tar-gz files (one per acquisition) and are also converted to a NIfTI file (also one per acquisition). P-files are copied into this same folder, and P-files from our custom PSDs (e.g., spiral and SMS-EPI) are reconstructed and the resulting images saved in a NIfTI. Physio data, if recorded, are saved on nims as well.		A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. The ''reapers'' are ever-running processes that reap images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''cnifs''') that's accessible via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. In '''nims''', the data are organized by the group name, an experiment name (both set at scan-time in the '''PatientID''' field), and exam date. Dicoms are archived in tar-gz files (one per acquisition) and are also converted to a NIfTI file (also one per acquisition). P-files are copied into this same folder, and P-files from our custom PSDs (e.g., spiral and SMS-EPI) are reconstructed and the resulting images saved in a NIfTI. Physio data, if recorded, are saved on nims as well.

	= Data Sharing =		= Data Sharing =

imported>Bobd at 17:30, 5 March 2014

2014-03-05T17:30:53Z

← Older revision		Revision as of 17:30, 5 March 2014
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	The CNI ~~is developing~~ an integrated neurobiological image management system (NIMS) to facilitate the stewardship of all data collected at the CNI. NIMS is currently under active development. ~~A preliminary version of NIMS (~~[https://cni.stanford.edu/nims/ NIMS ~~lite~~]) is currently deployed and used by all CNI users to securely access their scan data. This system is useful for organizing and archiving the data that users collect here.		The CNI has developed an integrated neurobiological image management system (NIMS) to facilitate the stewardship of all data collected at the CNI. NIMS is currently under active development. [https://cni.stanford.edu/nims/ NIMS 1.0]) is currently deployed and used by all CNI users to securely access their scan data. This system is useful for organizing and archiving the data that users collect here. NIMS 2.0 is currently under active development; check the status on [https://github.com/cni/nims/ github page].

	~~The~~ [https://cni~~.stanford.edu~~/~~nimsgears~~/ ~~new version of NIMS~~] is currently in beta testing. We suggest that all the CNI users give it a try. We will continue to run NIMS lite in parallel with the new version so that you can always go back there to get your data if something isn't working in the new system.

	For more information on our NIMS software development efforts, see the [[NIMS \| CNI Software Development page]].		For more information on our NIMS software development efforts, see the [[NIMS \| CNI Software Development page]].
Line 7:		Line 5:
	= mrReaper: Automatic data transfer to nims =		= mrReaper: Automatic data transfer to nims =

	A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. ''~~mrReaper~~'' is an ever-running processes that manage images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''~~nims~~''')~~. From there, the data are available to all authorized users~~ via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. On '''nims''', the data are organized by the ~~PI's Name~~, an ~~optional~~ experiment name (both set at scan-time in the '''PatientID''' field), and exam date~~. All data acquired during an exam are put into a folder with a name of the form ''YYYYMMDD_EXAMNUM''~~. Dicoms are archived in ~~zip~~ files (one per ~~series~~) and are also converted to a ~~NIFTI~~ file (also one per ~~series~~)~~, if possible~~. P-files are copied into this same folder, and P-files from our custom spiral ~~PSD~~ are ~~reconned~~ and ~~a NIFTI of~~ the resulting images ~~is also offered to the user~~. Physio data, if recorded, are saved on nims as well.		A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. The ''reaper'' is an ever-running processes that manage images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''cnifs''') that's accessible via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. In '''nims''', the data are organized by the group name, an experiment name (both set at scan-time in the '''PatientID''' field), and exam date. Dicoms are archived in tar-gz files (one per acquisition) and are also converted to a NIfTI file (also one per acquisition). P-files are copied into this same folder, and P-files from our custom PSDs (e.g., spiral and SMS-EPI) are reconstructed and the resulting images saved in a NIfTI. Physio data, if recorded, are saved on nims as well.

	= Data Sharing =		= Data Sharing =

imported>Lmperry: /* Sharing data with collaborators outside of Stanford */

2013-03-08T21:17:04Z

Sharing data with collaborators outside of Stanford

← Older revision		Revision as of 21:17, 8 March 2013
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	'''Outside collaborators'''		'''Outside collaborators'''
	<ol>		<ol>
	# Set up a SUNetID by visiting [http://accounts.stanford.edu Stanford Accounts] and choosing 'Create' -> 'I do not have a university ID' -> 'Continue without University ID'		<li>Set up a SUNetID by visiting [http://accounts.stanford.edu Stanford Accounts] and choosing 'Create' -> 'I do not have a university ID' -> 'Continue without University ID'</li>
	# Follow the steps to create a SUNET ID and pick a password, etc.		<li>Follow the steps to create a SUNET ID and pick a password, etc. </li>
			:Your SUNETID must:
			:*Be 3-8 characters long (lower-case letters and numbers only)
			:*Start with a letter
			:*We recommend: ''FirstinitialLastInstitution'' (e.g.: For Michael Perry @ Stanford sunetid = '''mperrysu''').
			:*For more info regarding SUNET IDs: http://itservices.stanford.edu/service/accounts/sunetids

	<br>		<li> Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.</li>
	~~Your SUNETID must: <br>~~		<li> After they have confirmed that they have granted you permission navigate to the NIMS interface, find the experiment with the data and drag it to the 'Download' icon. </li>
	*Be 3-8 characters long (lower-case letters and numbers only)
	*Start with a letter
	* We recommend:
	~~:''FirstinitialLastInstitution'' (e.g.: For Michael Perry @ Stanford sunetid = '''mperrysu''')~~

	~~For more info regarding SUNET IDs: http://itservices.stanford.edu/service/accounts/sunetids~~
	~~<br><br>~~

	# Once the SUNET ID is created, email your SUNET ID the collaborating Stanford PI; he/she must give you permission to access the data.
	# After they have confirmed that they have granted you permission navigate to the NIMS interface, find the experiment with the data and drag it to the 'Download' icon.
	</ol>		</ol>

imported>Wandell: /* Sharing data with collaborators outside of Stanford */

2013-03-08T21:05:03Z

Sharing data with collaborators outside of Stanford

← Older revision		Revision as of 21:05, 8 March 2013
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	*Start with a letter		*Start with a letter
	* We recommend:		* We recommend:
	:''FirstinitialLastInstitution''		:''FirstinitialLastInstitution'' (e.g.: For Michael Perry @ Stanford sunetid = '''mperrysu''')
	e.g.: For Michael Perry @ Stanford
	sunetid = '''mperrysu'''

	For more info regarding SUNET IDs: http://itservices.stanford.edu/service/accounts/sunetids		For more info regarding SUNET IDs: http://itservices.stanford.edu/service/accounts/sunetids