Flywheel - Revision history

Huawu: /* Downloading Data */

2026-03-18T20:36:43Z

Downloading Data

← Older revision		Revision as of 20:36, 18 March 2026
Line 134:		Line 134:

	= Downloading Data =		= Downloading Data =
	There are several ways to download data from Flywheel, including via the [//~~flywheelio~~.~~zendesk~~.~~com/hc~~/~~en-us~~/~~articles~~/~~360008622994-Downloading-sessions-or-acquisitions-from-the-Web-UI~~ WEB UI], the [//~~flywheelio~~.~~zendesk~~.~~com~~/~~hc/en-us/sections/360001596834-Command-Line-Interface~~ command line interface (CLI)], and the Flywheel SDK (which is available for both [//flywheel~~-io.github~~.io/~~core/branches~~/~~master~~/python~~/getting_started.html~~ Python] and [//flywheel~~-io.github~~.io/~~core~~/~~branches/master~~/matlab~~/getting_started.html~~ MATLAB]). The links below can help you get started with the various methods of export:		There are several ways to download data from Flywheel, including via the [https://docs.flywheel.io/data_transfer/outbound/ WEB UI], the [https://docs.flywheel.io/CLI command line interface (CLI)], and the Flywheel SDK (which is available for both [https://docs.flywheel.io/Developer_Guides/api_sdk/#python-sdk Python] and [https://docs.flywheel.io/Developer_Guides/api_sdk/#call-flywheel-sdk-from-matlab MATLAB]). The links below can help you get started with the various methods of export:

	=== UI Downloads ===		=== UI Downloads ===
	* [//~~flywheelio~~.~~zendesk~~.~~com~~/hc/~~en-us~~/~~articles/360009256973-Downloading-a-file~~ Download individual Files]		* [https://docs.flywheel.io/user/download/user_downloading_a_file_from_the_web_ui Download individual Files]
	* [//~~flywheelio~~.~~zendesk~~.~~com/hc~~/~~en-us~~/~~articles~~/~~360008622994-Downloading-sessions-or-acquisitions-from-the-Web-UI~~ Download session or acquisition containers]		* [https://docs.flywheel.io/user/download/user_downloading_sessions_or_acquisitions_from_web_ui Download session or acquisition containers]
	* [//~~flywheelio~~.~~zendesk~~.~~com/hc~~/~~en-us~~/~~articles~~/~~360008629794-Downloading-an-entire-project~~ Download a Project]		* [https://docs.flywheel.io/user/download/user_downloading_an_entire_project_from_the_web_ui Download a Project]


	=== Flywheel SDK ===		=== Flywheel SDK ===
	* [//flywheel~~-io.gitlab~~.io/~~product~~/~~backend~~/sdk~~/branches/master/~~matlab~~/index.html~~ MATLAB]		* [https://docs.flywheel.io/Developer_Guides/api_sdk/#call-flywheel-sdk-from-matlab MATLAB]
	* [//flywheel~~-io.gitlab~~.io/~~product~~/~~backend~~/sdk~~/branches/master/python/index.html~~ Python]		* [https://docs.flywheel.io/Developer_Guides/api_sdk/#python-sdk Python]
	* [//~~gitlab~~.~~com/~~flywheel-io/~~public~~/~~flywheel-tutorials~~ Support materials SDK examples (Jupyter notebooks)]		* [https://docs.flywheel.io/Developer_Guides/additional_information/jupyter_notebooks_python_sdk Support materials SDK examples (Jupyter notebooks)]

Huawu: /* CLI: Tips and Best Practices for CNI Users */

2026-03-18T20:25:46Z

CLI: Tips and Best Practices for CNI Users

← Older revision		Revision as of 20:25, 18 March 2026
Line 153:		Line 153:
	=== CLI: Tips and Best Practices for CNI Users ===		=== CLI: Tips and Best Practices for CNI Users ===

	This section focuses on a few tips for using the CLI to download your data. For a complete overview of the Flywheel CLI, including how to get started, please look through the [//docs.flywheel.io/~~hc/en-us/search?utf8=%E2%9C%93&query=~~CLI Flywheel CLI Documentation].		This section focuses on a few tips for using the CLI to download your data. For a complete overview of the Flywheel CLI, including how to get started, please look through the [https://docs.flywheel.io/CLI Flywheel CLI Documentation].

Huawu: /* Flywheel CLI */

2026-03-18T20:25:17Z

Flywheel CLI

← Older revision		Revision as of 20:25, 18 March 2026
Line 149:		Line 149:

	=== Flywheel CLI ===		=== Flywheel CLI ===
	* [//docs.flywheel.io/hc/~~en-us/search?utf8=%E2%9C%93&query=CLI~~ Flywheel CLI Documentation]		* [https://docs.flywheel.io/CLI/ Flywheel CLI Documentation]

	=== CLI: Tips and Best Practices for CNI Users ===		=== CLI: Tips and Best Practices for CNI Users ===

Akerr: /* Protected Health Information */

2026-02-02T18:59:38Z

Protected Health Information

← Older revision		Revision as of 18:59, 2 February 2026
Line 85:		Line 85:
	Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.		Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.

	Anonymized research data for publication can be shared without harm. See [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site]. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients. ~~Specifically, data~~ uploaded to Flywheel ~~strips information from these fields~~:		Anonymized research data for publication can be shared without harm. See [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site]. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients.

			It is our policy that users '''never''' use any PHI identifiers when conducting an MRI exam. We further strip out any field that may inadvertently include PHI before it is uploaded to Flywheel. This includes:

	* Patient ID field		* Patient ID field
Line 91:		Line 93:
	* Medical Record Number		* Medical Record Number
	* Subject Name (first and last)		* Subject Name (first and last)
			* Anything else that clearly identifies the human subject

			'''Our standard however is to never use any PHI identifiers when entering data into the scanner!'''

	~~For PIs, please note we do look for PHI information and~~ over the years we have found ~~that users sometimes insert names, phone numbers~~ and ~~other information that might identify the subject. When we find such information, we delete it. The most likely places that RAs and others insert this information are~~ these fields:		Be careful also about what you enter in these fields - over the years we have found (and deleted) PHI from these fields:

	* Subject code (part of Patient ID)		* Subject code (part of Patient ID)
Line 98:		Line 103:
	* Series description		* Series description

	~~Thus, we ask all CNI users: '''Never use any PHI identifiers when entering data into the scanner!'''~~		It is permissible to include the subject's weight which is needed for scanner safety calculations.

	It is permissible to include the subject's weight ~~and age up to some precision~~.

	At present, to describe the PHI methods in your publications, you might find this summary paragraph helpful.		At present, to describe the PHI methods in your publications, you might find this summary paragraph helpful.

	''Data at Stanford's Center for Cognitive and Neurobiological Imaging are securely transferred from the MR scanner directly to a data management system (Flywheel.io) that is running within a Google platform space that is approved for research data. Prior to transfer the data file headers are stripped of fields that may contain subject information (patient id, DOB, MRN, name fields). These procedures meet the Stanford standard for anonymized research data for publication and can be shared without harm. See: [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site].		''Data at Stanford's Center for Cognitive and Neurobiological Imaging are securely transferred from the MR scanner directly to a data management system (Flywheel.io) that is running within a Google platform space that is approved for research data. Prior to transfer the data file headers are stripped of fields that may contain subject information (patient id, DOB, MRN, name fields). These procedures meet the Stanford standard for anonymized research data for publication and can be shared without harm. See: [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site].

	'''N.B.''' Flywheel is planning to provide a substantial enhancement of the anonymization protocol so that each lab will have the ability to control the details of its own anonymization protocol. We will send a note describing the capabilities when the feature is released - which is expected first quarter 2021.

	= Data Processing =		= Data Processing =

Wandell: /* Default Gear Rules */

2023-08-23T17:38:15Z

Default Gear Rules

← Older revision		Revision as of 17:38, 23 August 2023
Line 113:		Line 113:


	== ~~Default~~ Gear Rules ==		== Gear Rules (Default) ==

	At CNI we have defined a default set of rules that are applied to every new project. Each rule defines the logic that must be satisfied in order for a given gear to be run on a data file.		At CNI we have defined a default set of rules that are applied to every new project. Each rule defines the logic that must be satisfied in order for a given gear to be run on a data file.
Line 120:		Line 120:

	[[File:GearRules.png\|600px\|thumb\|center\|Gear Rule Template]]		[[File:GearRules.png\|600px\|thumb\|center\|Gear Rule Template]]


	=== A special note on DICOM to NIfTI Conversion (dcm2niix & dcm-convert) ===		=== A special note on DICOM to NIfTI Conversion (dcm2niix & dcm-convert) ===

imported>Lmperry: /* Data Processing on Upload */

2021-06-25T17:26:49Z

Data Processing on Upload

@@ Line 108: / Line 108: @@
 '''N.B.'''  Flywheel is planning to provide a substantial enhancement of the anonymization protocol so that each lab will have the ability to control the details of its own anonymization protocol. We will send a note describing the capabilities when the feature is released - which is expected first quarter 2021.
-= Data Processing on Upload =
+= Data Processing =
-At upload time data are processed according to a given Project's "[//docs.flywheel.io/hc/en-us/articles/360008553133-Project-Gear-Rules Gear Rules]". For help with Gear rules please reach out to Michael Perry.
 = Downloading Data =

imported>Lmperry: /* Data upload */

2021-06-25T17:10:54Z

Data upload

← Older revision		Revision as of 17:10, 25 June 2021
Line 22:		Line 22:

	= Data upload =		= Data upload =
			The CNI scanner produces DICOM, P-File, and Physio data. The sequence you are using along with your scan parameters will determine which of those data are generated. Regardless of the type, those data will make their way into Flywheel automatically via one of the Connectors, described next.

	Flywheel ~~captures~~ data directly ~~from~~ the MR scanner ~~via its Connector technology. The scanner produces~~ DICOM (and P-File) data, and ~~those~~ data ~~are automatically packaged~~ and ~~uploaded~~ to Flywheel. ~~For~~ a ~~typical session~~, ~~series~~ data will be in Flywheel ~~before the session~~ has ~~ended~~.		== Connectors ==
			At the CNI data are uploaded to Flywheel automatically via Connectors (aka Reapers). CNI has multiple Flywheel Connectors running, one for each of the types of data that must make their way into Flywheel.

			The connectors running at CNI are:
			* DICOM connector - communicates directly with the scanner's DICOM server to "discover" new data, package those data, and upload those data to Flywheel
			* P-File connector - packages and transfers raw P-File data from the console to Flywheel.
			* Physio connector - packages and transfers physio data from the console to Flywheel. This connector attempts to match the physio data to the correct series/acquisition within Flywheel, however if the scan is ended early, or if the prescribed duration is off from the actual duration, the physio data may not be transferred or it may end up in the wrong series. Please be sure to check your physio data and report any issues to CNI staff right away.

			== Getting your data to the right place ==
			The Flywheel Connectors determine where to place data in the hierarchy using information entered into the MR console by the user and obtained from the DICOM or PFile data.

			We refer to the information provided by the user to help Flywheel understand where the data belong as the "Sort String". It is important to understand how to provide this information correctly so that your data find their way to your project without delay.

			If a mistake is made here, worry not, those data will still be uploaded to Flywheel, however they will go to a group and project which only CNI staff have access to. If you believe this has happened to you, please feel free to reach out to CNI staff and we will help get your data where it belongs.

	=== Flywheel Sort String (Good) ===		=== Flywheel Sort String (Good) ===
	~~The Flywheel Connector determines where to place data in the hierarchy using information either entered into the MR console by the user or obtained from the DICOM data.~~


	To make sure the data you collect is sent to the correct Flywheel project for your lab, you must enter a "Flywheel sort string" on the console.		To make sure the data you collect is sent to the correct Flywheel project for your lab, you must enter a "Flywheel sort string" on the console.
Line 54:		Line 66:

	=== Session Labels and Tags ===		=== Session Labels and Tags ===
	In some cases, users want to ~~control~~ the name of the session rather than have Flywheel use the default name.		In some cases, users want to set the name of the session rather than have Flywheel use the default name (which is the exam number).


	You can control the session name ~~using~~ the ''AdditionalPatientHistory'' section on the console.		You can control the session name/label by placing information in the ''AdditionalPatientHistory'' section on the console, like so:


	~~Set~~ the session label ~~and tags~~ using the following format (without the "<>"):		To set the '''session label'' using the following format (without the "<>"):

	label_<your_desired_session_label>		label_<your_desired_session_label>


	~~Flywheel~~ also ~~lets you~~ tag a session to make it easier to find ~~with its search function~~.		You may also '''tag a session''' to make it easier to find later. You can '''set a session tag''' by inserting this string in the ''AdditionalPatientHistory'' section.


	You can set a tag by inserting this string in the ''AdditionalPatientHistory'' section.

	tag_<tag_name>		tag_<tag_name>

imported>Wandell: /* Protected Health Information */

2020-11-13T22:08:52Z

Protected Health Information

← Older revision		Revision as of 22:08, 13 November 2020
Line 76:		Line 76:
	Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.		Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.

	Anonymized research data for publication can be shared without harm. See [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this site]. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients. Specifically, data uploaded to Flywheel strips information from these fields:		Anonymized research data for publication can be shared without harm. See [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site]. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients. Specifically, data uploaded to Flywheel strips information from these fields:

	* Patient ID field		* Patient ID field

imported>Wandell: /* Protected Health Information */

2020-11-13T22:08:20Z

Protected Health Information

← Older revision		Revision as of 22:08, 13 November 2020
Line 95:		Line 95:
	At present, to describe the PHI methods in your publications, you might find this summary paragraph helpful.		At present, to describe the PHI methods in your publications, you might find this summary paragraph helpful.

	''Data at Stanford's Center for Cognitive and Neurobiological Imaging are securely transferred from the MR scanner directly to a data management system (Flywheel.io) that is running within a Google platform space that is approved for research data. Prior to transfer the data file headers are stripped of fields that may contain subject information (patient id, DOB, MRN, name fields). These procedures meet the Stanford standard for anonymized research data for publication and can be shared without harm. See: //med.stanford.edu/irt/security/hipaa.html.''		''Data at Stanford's Center for Cognitive and Neurobiological Imaging are securely transferred from the MR scanner directly to a data management system (Flywheel.io) that is running within a Google platform space that is approved for research data. Prior to transfer the data file headers are stripped of fields that may contain subject information (patient id, DOB, MRN, name fields). These procedures meet the Stanford standard for anonymized research data for publication and can be shared without harm. See: [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this Stanford site].

	'''N.B.''' Flywheel is planning to provide a substantial enhancement of the anonymization protocol so that each lab will have the ability to control the details of its own anonymization protocol. We will send a note describing the capabilities when the feature is released - which is expected first quarter 2021.		'''N.B.''' Flywheel is planning to provide a substantial enhancement of the anonymization protocol so that each lab will have the ability to control the details of its own anonymization protocol. We will send a note describing the capabilities when the feature is released - which is expected first quarter 2021.

imported>Wandell: /* Protected Health Information */

2020-11-13T22:07:15Z

Protected Health Information

← Older revision		Revision as of 22:07, 13 November 2020
Line 76:		Line 76:
	Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.		Protected Health Information (PHI) is considered High Risk Data according to the Stanford Data Classification Guidelines. PHI is defined as any information that can be used to identify an individual and may relate to their past, present, or future health. By law, this information must be encrypted by law and must be (a) stored in encrypted form, and (b) transmitted only through secure means.

	Anonymized research data for publication can be shared without harm. See: //med.stanford.edu/irt/security/hipaa.html. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients. Specifically, data uploaded to Flywheel strips information from these fields:		Anonymized research data for publication can be shared without harm. See [https://med.stanford.edu/irt/security/stanfordinfo/hipaa.html this site]. Although CNI participants are not medical patients, we treat human subject data with the same PHI status as if they were patients. Specifically, data uploaded to Flywheel strips information from these fields:

	* Patient ID field		* Patient ID field