NIMS - Revision history

imported>Lmperry: /* Data Sorting */

2017-07-31T20:57:44Z

Data Sorting

← Older revision		Revision as of 20:57, 31 July 2017
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	<SUBJECT_ID>@<GROUP_NAME>/<PROJECT_NAME>		<SUBJECT_ID>@<GROUP_NAME>/<PROJECT_NAME>

	Note the special characters ('@' between the SUBJECT_ID and the GROUP_NAME and the '/' between the GROUP_NAME and PROJECT_NAME. When a unique SUBJECT_ID is not being given the '@" can be omitted.		** Note the special characters ('@' between the SUBJECT_ID and the GROUP_NAME and the '/' between the GROUP_NAME and PROJECT_NAME.
			When a unique SUBJECT_ID is not being given the '@" can be omitted.

	Those exams that do not provide sorting information will be placed into an 'Unknown' Group within an 'Untitled' Project. Those data can be rearranged by a CNI staff member.		Those exams that do not provide sorting information will be placed into an 'Unknown' Group within an 'Untitled' Project. Those data can be rearranged by a CNI staff member.

imported>Lmperry: /* Data Sorting */

2017-07-31T20:57:27Z

Data Sorting

← Older revision		Revision as of 20:57, 31 July 2017
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	The format of the string in the '''Patient ID''' field is as follows:		The format of the string in the '''Patient ID''' field is as follows:
	<SUBJECT_ID>@<GROUP_NAME>/<PROJECT_NAME>		<SUBJECT_ID>@<GROUP_NAME>/<PROJECT_NAME>

			Note the special characters ('@' between the SUBJECT_ID and the GROUP_NAME and the '/' between the GROUP_NAME and PROJECT_NAME. When a unique SUBJECT_ID is not being given the '@" can be omitted.

	Those exams that do not provide sorting information will be placed into an 'Unknown' Group within an 'Untitled' Project. Those data can be rearranged by a CNI staff member.		Those exams that do not provide sorting information will be placed into an 'Unknown' Group within an 'Untitled' Project. Those data can be rearranged by a CNI staff member.

			For those exams which the operator does not wish to be in NIMS she should simply type 'Discard' into the '''Patient ID''' field.

	= NIMS Access Control =		= NIMS Access Control =

imported>Lmperry at 20:54, 31 July 2017

2017-07-31T20:54:06Z

← Older revision		Revision as of 20:54, 31 July 2017
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	NIMS imposes a particular organization on the data that it houses. The core container for data is the '''experiment'''. An experiment is simply a collection of datasets that share a common description and common access-control rights (see below). Within an experiment, the most common type of data is a '''session'''. This is loosely defined as a short period of time when a research subject visits the lab for data collection. Within a session, there may be several '''epochs''', which are well-defined chunks of time that involved measurement. The most common type of epoch is an MR scan. Such an epoch would include the MR '''dataset''' acquired during that scan, as well as any other data that was time-synchronized to the epoch, such as behavioral data, physiological data, eye tracking data, EEG data, etc.		NIMS imposes a particular organization on the data that it houses. The core container for data is the '''experiment'''. An experiment is simply a collection of datasets that share a common description and common access-control rights (see below). Within an experiment, the most common type of data is a '''session'''. This is loosely defined as a short period of time when a research subject visits the lab for data collection. Within a session, there may be several '''epochs''', which are well-defined chunks of time that involved measurement. The most common type of epoch is an MR scan. Such an epoch would include the MR '''dataset''' acquired during that scan, as well as any other data that was time-synchronized to the epoch, such as behavioral data, physiological data, eye tracking data, EEG data, etc.

	== Data Sorting ==		= Data Sorting =
	NIMS is programmed to sort data according to information provided by the operator within the '''Patient ID''' field. Within this field you may provide your Group and Project name as well as (optionally) a unique subject identifier.		NIMS is programmed to sort data according to information provided by the operator within the '''Patient ID''' field. Within this field you may provide your Group and Project name as well as (optionally) a unique subject identifier.

imported>Lmperry at 20:53, 31 July 2017

2017-07-31T20:53:55Z

← Older revision		Revision as of 20:53, 31 July 2017
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	* [http://surfer.nmr.mgh.harvard.edu/ FreeSurfer] tissue segmentation, [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheSurface-basedStream surface fitting], and [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream surface labeling]		* [http://surfer.nmr.mgh.harvard.edu/ FreeSurfer] tissue segmentation, [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheSurface-basedStream surface fitting], and [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream surface labeling]
	* BrainPrint: a compact ID code that identifies and distinguishes each unique brain (useful for reliably finding all the datasets collected on a single subject)		* BrainPrint: a compact ID code that identifies and distinguishes each unique brain (useful for reliably finding all the datasets collected on a single subject)

	~~= User Feedback =~~

	~~== Feedback from first CNI user meeting ==~~

	* Take over another scanner field for subject ID
	* fix NIFTI TR field, add TE, etc.
	* copy of the protocol
	* add MR parameter fields to the database
	* show/search for age, gender, operator, sequence type

	~~== March 16, 2012 CNI user meeting ==~~

	* Turn off view of all users for new users with no permissions
	* filtering of user lists (especially unaffiliated user lists)
	* Download functionality
	* Search functionality

	* Log of who does what

imported>Lmperry: /* NIMS Data Organization Overview */

2017-07-31T20:52:59Z

NIMS Data Organization Overview

← Older revision		Revision as of 20:52, 31 July 2017
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	[[Image:NIMS_Organization_overview.png\|thumb\|300px\|right\|NIMS data organization.]]		[[Image:NIMS_Organization_overview.png\|thumb\|300px\|right\|NIMS data organization.]]
	NIMS imposes a particular organization on the data that it houses. The core container for data is the '''experiment'''. An experiment is simply a collection of datasets that share a common description and common access-control rights (see below). Within an experiment, the most common type of data is a '''session'''. This is loosely defined as a short period of time when a research subject visits the lab for data collection. Within a session, there may be several '''epochs''', which are well-defined chunks of time that involved measurement. The most common type of epoch is an MR scan. Such an epoch would include the MR '''dataset''' acquired during that scan, as well as any other data that was time-synchronized to the epoch, such as behavioral data, physiological data, eye tracking data, EEG data, etc.		NIMS imposes a particular organization on the data that it houses. The core container for data is the '''experiment'''. An experiment is simply a collection of datasets that share a common description and common access-control rights (see below). Within an experiment, the most common type of data is a '''session'''. This is loosely defined as a short period of time when a research subject visits the lab for data collection. Within a session, there may be several '''epochs''', which are well-defined chunks of time that involved measurement. The most common type of epoch is an MR scan. Such an epoch would include the MR '''dataset''' acquired during that scan, as well as any other data that was time-synchronized to the epoch, such as behavioral data, physiological data, eye tracking data, EEG data, etc.

			== Data Sorting ==
			NIMS is programmed to sort data according to information provided by the operator within the '''Patient ID''' field. Within this field you may provide your Group and Project name as well as (optionally) a unique subject identifier.

			The format of the string in the '''Patient ID''' field is as follows:
			<SUBJECT_ID>@<GROUP_NAME>/<PROJECT_NAME>

			Those exams that do not provide sorting information will be placed into an 'Unknown' Group within an 'Untitled' Project. Those data can be rearranged by a CNI staff member.

	= NIMS Access Control =		= NIMS Access Control =

imported>Bobd: /* March 16, 2012 user meeting */

2013-03-07T17:23:20Z

March 16, 2012 user meeting

← Older revision		Revision as of 17:23, 7 March 2013
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	* show/search for age, gender, operator, sequence type		* show/search for age, gender, operator, sequence type

	== March 16, 2012 user meeting ==		== March 16, 2012 CNI user meeting ==

	* Turn off view of all users for new users with no permissions		* Turn off view of all users for new users with no permissions

imported>Bobd: /* Feedback from first user meeting */

2013-03-07T17:23:12Z

Feedback from first user meeting

← Older revision		Revision as of 17:23, 7 March 2013
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	= User Feedback =		= User Feedback =

	== Feedback from first user meeting ==		== Feedback from first CNI user meeting ==

	* Take over another scanner field for subject ID		* Take over another scanner field for subject ID
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	* add MR parameter fields to the database		* add MR parameter fields to the database
	* show/search for age, gender, operator, sequence type		* show/search for age, gender, operator, sequence type


	== March 16, 2012 user meeting ==		== March 16, 2012 user meeting ==

imported>Bobd: /* The purpose of NIMS */

2013-03-07T17:20:31Z

The purpose of NIMS

← Older revision		Revision as of 17:20, 7 March 2013
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	= The purpose of NIMS =		= The purpose of NIMS =
	As a service to our users (and to scientific community!), the CNI is committed to archiving all data collected at the center. We plan to archive all the reconstructed data ~~forever~~. For some sequences, we will also archive the k-space data for at least two years. Thus, the primary aim of NIMS is to store the data collected at the CNI ~~in an organized way~~ and allow easy access. NIMS is ~~also~~ an open-source ~~pacage~~, and we hope that other imaging centers will use it and perhaps contribute to the code.		As a service to our users (and to the scientific community!), the CNI is committed to archiving all data collected at the center. We plan to archive all the reconstructed data in perpetuity. For some sequences, we will also archive the k-space data for at least two years. Thus, the primary aim of NIMS is to store and organize the data collected at the CNI and allow easy access by the data owners. NIMS also does some minimal data preprocessing, such as conversion from DICOM to NIFTI format, reconstruction of k-space data for sequences that require a custom recon, and calculation of physiological regressors when physio data have been recorded. NIMS is an open-source package, and we hope that other imaging centers will use it and perhaps contribute to the code.

	We also intend NIMS to facilitate data sharing between labs, both within Stanford and across institutions. To this end, the CNI is collaborating with [https://www.ibic.washington.edu/wiki/display/public/About+IBIC a group at the University of Washington] on a data sharing initiative (SNI).		We also intend NIMS to facilitate data sharing between labs, both within Stanford and across institutions. To this end, the CNI is collaborating with [https://www.ibic.washington.edu/wiki/display/public/About+IBIC a group at the University of Washington] on a data sharing initiative (SNI).

imported>Bobd: /* User Feedback */

2012-03-17T00:38:20Z

User Feedback

← Older revision		Revision as of 00:38, 17 March 2012
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	= User Feedback =		= User Feedback =

	~~Please list your ideas here!~~		== Feedback from first user meeting ==


	* Take over another scanner field for subject ID		* Take over another scanner field for subject ID
			* fix NIFTI TR field, add TE, etc.
			* copy of the protocol
			* add MR parameter fields to the database
			* show/search for age, gender, operator, sequence type

	* fix NIFTI TR field, add TE, etc.

	* copy of the protocol		== March 16, 2012 user meeting ==

	* ~~add MR parameter fields to the database~~		* Turn off view of all users for new users with no permissions
			* filtering of user lists (especially unaffiliated user lists)
			* Download functionality
			* Search functionality

	* ~~show/search for age, gender, operator, sequence type~~		* Log of who does what

imported>Gsfr: /* User Feedback */

2012-01-21T05:54:37Z

User Feedback

← Older revision		Revision as of 05:54, 21 January 2012
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	* add MR parameter fields to the database		* add MR parameter fields to the database

	* show/search for age		* show/search for age, gender, operator, sequence type