QA - Revision history

Huawu: /* Subject Motion */

2026-03-18T20:55:25Z

Subject Motion

← Older revision		Revision as of 20:55, 18 March 2026
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	==Subject Motion==		==Subject Motion==
	Subject motion is estimated using [~~http~~://nipy.org/nipy~~/stable~~/api/generated/nipy.algorithms.registration.groupwise_registration.html FmriRealign4d] (without slice-time correction). A plot of the mean displacement, both absolute and relative, is presented. Absolute displacement is the mean displacement relative to the middle frame. Relative displacement is the mean displacement relative to the previous frame. (Mean displacement is computed using [http://www.fmrib.ox.ac.uk/analysis/techrep/tr99mj1/tr99mj1/index.html Mark Jenkinson's algorithm].)		Subject motion is estimated using [https://nipy.org/nipy/api/generated/nipy.algorithms.registration.groupwise_registration.html FmriRealign4d] (without slice-time correction). A plot of the mean displacement, both absolute and relative, is presented. Absolute displacement is the mean displacement relative to the middle frame. Relative displacement is the mean displacement relative to the previous frame. (Mean displacement is computed using [http://www.fmrib.ox.ac.uk/analysis/techrep/tr99mj1/tr99mj1/index.html Mark Jenkinson's algorithm].)

	==Timeseries z-score==		==Timeseries z-score==

Huawu: /* Temporal SNR */

2026-03-18T20:53:52Z

Temporal SNR

← Older revision		Revision as of 20:53, 18 March 2026
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	==Temporal SNR==		==Temporal SNR==
	This is the median tSNR of all brain voxels (as defined by the [~~http~~://~~nipy~~.org/~~dipy~~/~~examples_built~~/~~brain_extraction_dwi~~.html median_otsu algorithm]). The tSNR is computed after the data have been motion-corrected (details below) and the slow-drift has been removed using a 3rd-order polynomial. Note that tSNR is very sensitive to voxel size, with bigger voxels generally producing higher tSNR. The acceleration factor will also affect tSNR (both inplane acceleration and slice multiplex acceleration), with more acceleration leading to lower tSNR. It is also somewhat sensitive to the TR (with longer TRs producing slightly higher tSNR). So it's a useful metric for comparison across scans with the same voxel size, TR and acceleration, but not useful for comparing across scans with different parameters.		This is the median tSNR of all brain voxels (as defined by the [https://docs.dipy.org/dev/reference_cmd/dipy_median_otsu.html median_otsu algorithm]). The tSNR is computed after the data have been motion-corrected (details below) and the slow-drift has been removed using a 3rd-order polynomial. Note that tSNR is very sensitive to voxel size, with bigger voxels generally producing higher tSNR. The acceleration factor will also affect tSNR (both inplane acceleration and slice multiplex acceleration), with more acceleration leading to lower tSNR. It is also somewhat sensitive to the TR (with longer TRs producing slightly higher tSNR). So it's a useful metric for comparison across scans with the same voxel size, TR and acceleration, but not useful for comparing across scans with different parameters.

	==Spike count==		==Spike count==

Huawu at 00:44, 12 February 2026

2026-02-12T00:44:12Z

← Older revision		Revision as of 00:44, 12 February 2026
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	Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the file list for an acquisition on ~~Flwwheel~~ within an hour after the scan finishes.		Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the file list for an acquisition on Flywheel within an hour after the scan finishes.

	=Finding the QA report=		=Finding the QA report=

	[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on ~~Flwwheel~~.]]		[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flywheel.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, use Flywheel's built-in viewer to open the motion and spike plots, as well as the global QA values in the json file.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, use Flywheel's built-in viewer to open the motion and spike plots, as well as the global QA values in the json file.

Huawu: Undo revision 59403 by Huawu (talk)

2026-02-12T00:43:46Z

Undo revision 59403 by Huawu (talk)

← Older revision		Revision as of 00:43, 12 February 2026
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	Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the ~~"datasets" column in the NIMS browser page~~ within an hour after the scan finishes.		Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the file list for an acquisition on Flwwheel within an hour after the scan finishes.

	=Finding the QA report=		=Finding the QA report=
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	[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]		[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, ~~double~~-~~click the QA dataset and a pop-over will~~ open ~~showing~~ the motion and spike plots, as well as ~~some~~ global QA values.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, use Flywheel's built-in viewer to open the motion and spike plots, as well as the global QA values in the json file.

	=What's in the QA report=		=What's in the QA report=
	The QA code is still under active development, so we will likely be adding more metrics to the report in the near future. Right now, the report will give you the QA version number (the version of the QA script that was used to generate the report), as well as the following information:

	==Temporal SNR==		==Temporal SNR==

Huawu at 00:43, 12 February 2026

2026-02-12T00:43:11Z

← Older revision		Revision as of 00:43, 12 February 2026
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	Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the ~~file list for an acquisition on Flwwheel~~ within an hour after the scan finishes.		Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the "datasets" column in the NIMS browser page within an hour after the scan finishes.

	=Finding the QA report=		=Finding the QA report=
Line 5:		Line 5:
	[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]		[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, ~~use Flywheel's built~~-~~in viewer to~~ open the motion and spike plots, as well as ~~the~~ global QA values ~~in the json file~~.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.

	=What's in the QA report=		=What's in the QA report=
			The QA code is still under active development, so we will likely be adding more metrics to the report in the near future. Right now, the report will give you the QA version number (the version of the QA script that was used to generate the report), as well as the following information:

	==Temporal SNR==		==Temporal SNR==

Huawu at 00:42, 12 February 2026

2026-02-12T00:42:46Z

← Older revision		Revision as of 00:42, 12 February 2026
Line 1:		Line 1:
	Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the ~~"datasets" column in the NIMS browser page~~ within an hour after the scan finishes.		Quality Assurance (QA) reports are generated for all functional MR data acquired at the CNI. These reports should appear in the file list for an acquisition on Flwwheel within an hour after the scan finishes.

	=Finding the QA report=		=Finding the QA report=
Line 5:		Line 5:
	[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]		[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, ~~double~~-~~click the QA dataset and a pop-over will~~ open ~~showing~~ the motion and spike plots, as well as ~~some~~ global QA values.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, use Flywheel's built-in viewer to open the motion and spike plots, as well as the global QA values in the json file.

	=What's in the QA report=		=What's in the QA report=
	The QA code is still under active development, so we will likely be adding more metrics to the report in the near future. Right now, the report will give you the QA version number (the version of the QA script that was used to generate the report), as well as the following information:

	==Temporal SNR==		==Temporal SNR==

Huawu: /* Finding the QA report */

2026-02-12T00:11:25Z

Finding the QA report

← Older revision		Revision as of 00:11, 12 February 2026
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	=Finding the QA report=		=Finding the QA report=

	[[File:Flywheel_QA.png\|thumb\|QA reports appear in the ~~datasets column of NIMS~~.]]		[[File:Flywheel_QA.png\|thumb\|QA reports appear in the file list for an acquisition on Flwwheel.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.

Huawu: /* Finding the QA report */

2026-02-12T00:08:38Z

Finding the QA report

← Older revision		Revision as of 00:08, 12 February 2026
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	=Finding the QA report=		=Finding the QA report=

	[[File:~~NIMS_QA~~.png\|thumb\|QA reports appear in the datasets column of NIMS.]]		[[File:Flywheel_QA.png\|thumb\|QA reports appear in the datasets column of NIMS.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.

Wandell: /* Finding the QA report */

2023-08-23T17:38:58Z

Finding the QA report

← Older revision		Revision as of 17:38, 23 August 2023
Line 2:		Line 2:

	=Finding the QA report=		=Finding the QA report=

	[[File:NIMS_QA.png\|thumb\|QA reports appear in the datasets column of NIMS.]]		[[File:NIMS_QA.png\|thumb\|QA reports appear in the datasets column of NIMS.]]

	The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.		The QA reports take anywhere from a few minutes to an hour to compute, depending on the scan resolution and duration. To view the report, double-click the QA dataset and a pop-over will open showing the motion and spike plots, as well as some global QA values.

imported>Bobd: /* Examples of QA reports */

2014-03-22T23:50:34Z

Examples of QA reports

← Older revision		Revision as of 23:50, 22 March 2014
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	=Examples of QA reports=		=Examples of QA reports=
	A good subject and well-behaved scanner:		A good subject and well-behaved scanner:
	[[Image: qa_good.~~jpg~~\| 650px]]		[[Image: qa_good.png\| 650px]]

	A bad subject and well-behaved scanner:		A bad subject and well-behaved scanner:
	[[Image: qa_motion.~~jpg~~\| 650px]]		[[Image: qa_motion.png\| 650px]]

	A good subject and spikey scanner:		A good subject and spikey scanner:
	[[Image: qa_spikes.~~jpg~~\| 650px]]		[[Image: qa_spikes.png\| 650px]]


	=Technical Details=		=Technical Details=
	The QA report generation code is part of the NIMS codebase and is [https://github.com/cni/nims/blob/master/nimsproc/qa_report.py available on Github].		The QA report generation code is part of the NIMS codebase and is [https://github.com/cni/nims/blob/master/nimsproc/qa_report.py available on Github].