Suggested Pipelines - Revision history

Nugenta: /* Advanced Coregistration SAM Pipeline */

2019-03-20T19:29:19Z

Advanced Coregistration SAM Pipeline

← Older revision		Revision as of 15:29, 20 March 2019
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	end		end
	}}		}}








	{{#mermaid:graph LR

	marks --> Covariance;

	subgraph MEG Preprocessing
	raw[Raw MEG data] --> filter[Basic Filtering];
	adc[Raw ADC/PPT<br>data] --> ThresholdDetect;
	ThresholdDetect --> marks[Create Markers];
	filter --> meg[MEG Data];
	end

	subgraph MEG Data Statistics
	meg --> Filter[Band-pass<br>filter];
	Filter --> Covariance;
	end

	}}

	{{#mermaid:graph LR
	subgraph Synthetic Aperture Magnetometry
	Covariance --> Beamformer;
	head[Head Model] --> Beamformer;
	Beamformer --> image["3D Images"];
	end
	}}

	{{#mermaid:graph LR
	subgraph SAM Workflow
	sam_cov --> sam_wts;
	sam_wts --> sam_3d;
	sam_3d --> AFNI;
	AFNI --> sam_wts;
	AFNI --> sam_cov;

	style sam_cov fill:#fcf
	click sam_cov "https://megcore.nih.gov/index.php/Sam_cov" "sam documentation"
	style sam_wts fill:#fcf
	click sam_wts "https://megcore.nih.gov/index.php/Sam_wts" "sam documentation"
	style sam_3d fill:#fcf
	click sam_3d "https://megcore.nih.gov/index.php/Sam_3d" "sam documentation"
	style AFNI fill:#fcf
	click AFNI "https://afni.nimh.nih.gov/" "The AFNI website"
	end
	}}

	# Create covariance matrices using sam_cov.
	# Compute beamformer weights with sam_wts.
	# sam_3d uses the weights to compute volumetric images of activity estimates.
	# View them with AFNI.
	# It didn't work, go back and try again.
	# Nope, still didn't work, try this instead.

Nugenta: /* Advanced Coregistration SAM Pipeline */

2019-03-20T19:28:52Z

Advanced Coregistration SAM Pipeline

← Older revision		Revision as of 15:28, 20 March 2019
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	== Advanced Coregistration SAM Pipeline ==		== Advanced Coregistration SAM Pipeline ==

			There is a limit to the accuracy with which MEG and MRI data can be coregistered using fiducial markers alone. One significant confounding issue is that the brain will be in a slightly different position inside the head in a seated position vs. a supine position. This pipeline describes using sam_coreg to refine the approximate fiducial placements. Once sam_coreg has been performed, the user can either do a traditional analysis using the SAM tools discussed previously, or make use of the programs that leverage the cortical data (patch_wts and roi_wts).

	{{#mermaid:graph LR		{{#mermaid:graph LR

Nugenta: /* Localizing Epileptiform Activity */

2019-03-20T19:25:04Z

Localizing Epileptiform Activity

← Older revision		Revision as of 15:25, 20 March 2019
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	== Localizing Epileptiform Activity ==		== Localizing Epileptiform Activity ==

			This describes localizing epileptiform activity from continuous datasets using excess kurtosis. First, a SAM analysis is performed with a relatively narrow bandwidth, 20-70Hz. The program sam_epi is used to produce images of kurtosis, and NIFTIpeak is used to find extrema in the images that may indicate voxels which contain spikes. Once targets are identified, the SAM analysis is essentially run again, this time with a wide bandwidth, on only those specific targets. DataEditor can read the weights for those targets and compute "virtual sensors" at those voxel locations. The epileptologist can then examine the time series and mark epileptic spikes.

	{{#mermaid:graph LR		{{#mermaid:graph LR
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	}}		}}


	== Advanced Coregistration SAM Pipeline ==		== Advanced Coregistration SAM Pipeline ==

Nugenta: /* Advanced Coregistration SAM Pipeline */

2019-03-20T19:21:42Z

Advanced Coregistration SAM Pipeline

← Older revision		Revision as of 15:21, 20 March 2019
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	FreeSurfer --> FSNormals.py		FreeSurfer --> FSNormals.py
	style FSNormals.py fill:#fcf		style FSNormals.py fill:#fcf
	click FSNormals.py "https://megcore.nih.gov/index.php/FSNormals.py" "~~sam~~ documentation"		click FSNormals.py "https://megcore.nih.gov/index.php/FSNormals.py" "FSNormals.py documentation"
	end		end

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	MEG-->sam_cov		MEG-->sam_cov
	style sam_cov fill:#fcf		style sam_cov fill:#fcf
	click sam_cov "https://megcore.nih.gov/index.php/Sam_cov" "~~sam~~ documentation"		click sam_cov "https://megcore.nih.gov/index.php/Sam_cov" "sam_cov documentation"

	subgraph MEGproc		subgraph MEGproc
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	sam_wts-->sam_power["sam_power"]		sam_wts-->sam_power["sam_power"]
	style sam_3d fill:#fcf		style sam_3d fill:#fcf
	click sam_3d "https://megcore.nih.gov/index.php/sam_3d_and_sam_3dc" "~~sam~~ documentation"		click sam_3d "https://megcore.nih.gov/index.php/sam_3d_and_sam_3dc" "sam_3d documentation"
	style sam_4d fill:#fcf		style sam_4d fill:#fcf
	click sam_4d "https://megcore.nih.gov/index.php/sam_4d_and_sam_4dc" "~~sam~~ documentation"		click sam_4d "https://megcore.nih.gov/index.php/sam_4d_and_sam_4dc" "sam_4d documentation"
	style sam_ers fill:#fcf		style sam_ers fill:#fcf
	click sam_ers "https://megcore.nih.gov/index.php/roi_wts" "~~sam~~ documentation"		click sam_ers "https://megcore.nih.gov/index.php/roi_wts" "sam_ers documentation"
	style sam_power fill:#fcf		style sam_power fill:#fcf
	click sam_power "https://megcore.nih.gov/index.php/sam_power" "sam_power documentation"		click sam_power "https://megcore.nih.gov/index.php/sam_power" "sam_power documentation"

Nugenta: /* Advanced Coregistration SAM Pipeline */

2019-03-20T19:12:12Z

Advanced Coregistration SAM Pipeline

← Older revision		Revision as of 15:12, 20 March 2019
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	style FSNormals.py fill:#fcf		style FSNormals.py fill:#fcf
	click FSNormals.py "https://megcore.nih.gov/index.php/FSNormals.py" "sam documentation"		click FSNormals.py "https://megcore.nih.gov/index.php/FSNormals.py" "sam documentation"

	end		end

	FSNormals.py --> sam_coreg		FSNormals.py --> sam_coreg
	MEG-->sam_cov		MEG-->sam_cov
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	style sam_power fill:#fcf		style sam_power fill:#fcf
	click sam_power "https://megcore.nih.gov/index.php/sam_power" "sam_power documentation"		click sam_power "https://megcore.nih.gov/index.php/sam_power" "sam_power documentation"
			end
	}}		}}

Nugenta: /* Advanced Coregistration SAM Pipeline */

2019-03-20T19:03:40Z

Advanced Coregistration SAM Pipeline

← Older revision		Revision as of 15:03, 20 March 2019
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	sam_coreg--> patch_wts		sam_coreg--> patch_wts
	sam_coreg--> roi_wts		sam_coreg--> roi_wts
			sam_coreg--> sam_wts
	style sam_coreg fill:#fcf		style sam_coreg fill:#fcf
	click sam_coreg "https://megcore.nih.gov/index.php/sam_coreg" "~~sam~~ documentation"		click sam_coreg "https://megcore.nih.gov/index.php/sam_coreg" "sam_coreg documentation"
	style patch_wts fill:#fcf		style patch_wts fill:#fcf
	click patch_wts "https://megcore.nih.gov/index.php/patch_wts" "~~sam~~ documentation"		click patch_wts "https://megcore.nih.gov/index.php/patch_wts" "patch_wts documentation"
	style roi_wts fill:#fcf		style roi_wts fill:#fcf
	click roi_wts "https://megcore.nih.gov/index.php/roi_wts" "~~sam~~ documentation"		click roi_wts "https://megcore.nih.gov/index.php/roi_wts" "roi_wts documentation"
			style sam_wts fill:#fcf
			click sam_wts "https://megcore.nih.gov/index.php/sam_wts" "sam_wts documentation"
	end		end

			subgraph SAM
			sam_wts-->sam_3d["sam_3d or sam_3dc"]
			sam_wts-->sam_4d["sam_4d or sam_4dc"]
			sam_wts-->sam_ers["sam_ers or sam_ersc"]
			sam_wts-->sam_power["sam_power"]
			style sam_3d fill:#fcf
			click sam_3d "https://megcore.nih.gov/index.php/sam_3d_and_sam_3dc" "sam documentation"
			style sam_4d fill:#fcf
			click sam_4d "https://megcore.nih.gov/index.php/sam_4d_and_sam_4dc" "sam documentation"
			style sam_ers fill:#fcf
			click sam_ers "https://megcore.nih.gov/index.php/roi_wts" "sam documentation"
			style sam_power fill:#fcf
			click sam_power "https://megcore.nih.gov/index.php/sam_power" "sam_power documentation"
	}}		}}

Nugenta: /* Advanced Coregistration Pipeline */

2019-03-20T18:54:42Z

Advanced Coregistration Pipeline

← Older revision		Revision as of 14:54, 20 March 2019
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	== Advanced Coregistration Pipeline ==		== Advanced Coregistration SAM Pipeline ==

	{{#mermaid:graph LR		{{#mermaid:graph LR
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	subgraph MEGproc		subgraph MEGproc
	sam_cov-->sam_coreg		sam_cov-->sam_coreg
	sam_coreg--> ~~sam_wts~~		sam_coreg--> patch_wts
			sam_coreg--> roi_wts
	style sam_coreg fill:#fcf		style sam_coreg fill:#fcf
	click sam_coreg "https://megcore.nih.gov/index.php/sam_coreg" "sam documentation"		click sam_coreg "https://megcore.nih.gov/index.php/sam_coreg" "sam documentation"
	style ~~sam_wts~~ fill:#fcf		style patch_wts fill:#fcf
	click ~~sam_wts~~ "https://megcore.nih.gov/index.php/~~sam_wts~~" "sam documentation"		click patch_wts "https://megcore.nih.gov/index.php/patch_wts" "sam documentation"
			style roi_wts fill:#fcf
			click roi_wts "https://megcore.nih.gov/index.php/roi_wts" "sam documentation"
	end		end

Nugenta: /* Advanced Coregistration Pipeline */

2019-03-20T18:53:03Z

Advanced Coregistration Pipeline

← Older revision		Revision as of 14:53, 20 March 2019
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	MRI["Structural MRI"] --> fids["Place Approximate <br> Fiducials"];		MRI["Structural MRI"] --> fids["Place Approximate <br> Fiducials"];
	fids --> FreeSurfer

	subgraph MRIproc		subgraph MRIproc

Nugenta: /* Advanced Coregistration Pipeline */

2019-03-20T18:52:42Z

Advanced Coregistration Pipeline

← Older revision		Revision as of 14:52, 20 March 2019
Line 152:		Line 152:

	MRI["Structural MRI"] --> fids["Place Approximate <br> Fiducials"];		MRI["Structural MRI"] --> fids["Place Approximate <br> Fiducials"];
	~~MRI~~--> FreeSurfer		fids --> FreeSurfer

	subgraph MRIproc		subgraph MRIproc

Nugenta: /* Advanced Coregistration Pipeline */

2019-03-20T18:52:16Z

Advanced Coregistration Pipeline

← Older revision		Revision as of 14:52, 20 March 2019
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	subgraph MRIproc		subgraph MRIproc
	fids ---> FreeSurfer		fids --> FreeSurfer
	FreeSurfer --> FSNormals.py		FreeSurfer --> FSNormals.py
	style FSNormals.py fill:#fcf		style FSNormals.py fill:#fcf