Suggested Pipelines

Master Pipeline

{{#mermaid:graph LR

 DoStuff --> DoMoreStuff;
 DoMoreStuff --> DoEvenMoreStuff;
 DoEvenMoreStuff --> PublishNaturePaper;

}}

Basic MRI Pre-Processing Workflow

For any experiment where you wish to localize data to the brain, the first step is MRI pre-processing. First, MEG data must be co-registered to the space of the MRI, either by manually placing fiducial points on the MRI, or through a semi-automated method where a digital head shape is aligned with a head surface. (Other algorithmic techniques are possible, these will be discussed later). For the purpose of source space reconstruction, the head can be modeled either as a collection of spheres, one per channel, (MultiSphere) or in a realistic fashion using the Nolte model.

{{#mermaid:graph LR

 MRI["Structural MRI"] --> fids["Place Fiducials"];
 MRI["Structural MRI"] --> shape["Register point clouds"];

subgraph MRI Preprocessing

 fids --> hull["Process with orthohull"];
 shape --> hull;

 style hull fill:#fcf
 click hull "https://megcore.nih.gov/index.php/Head_Localization_and_MRI_Coregistration" "orthohull documentation"

end

subgraph MultiSphere

 hull --> localSpheres;
 localSpheres --> MultiSphere["default.hdm"];

end

subgraph Nolte

 hull --> Nolte["hull.shape"];

end }}

Basic Resting State MEG processing

Basic preprocessing of resting state MEG data includes filtering, and possibly artifact removal. Removing artifacts could consist of eliminating bad segments, or a more comprehensive process like ICA. When examining resting state data, the end goals is usually to examine either static measures of power, or connectivity. For connectivity, the output of SAM is a continuous time series, usually the Hilbert envelope of a band limited signal. Following calculation of this time series, other routines (such as ICA, seed based correlation, etc.) can be used to derive connectivity between regions.

{{#mermaid:graph LR

   MEG["MEG Data"] --> Filtering;

subgraph PreProcessing

 Filtering --> Art["Artifact Removal"];

end

subgraph SAM PreProcessing

 Art --> sam_cov
 sam_cov --> sam_wts
 style sam_cov fill:#fcf
 style sam_wts fill:#fcf
 click sam_cov "https://megcore.nih.gov/index.php/Sam_cov" "sam_cov documentation"
 click sam_wts "https://megcore.nih.gov/index.php/Sam_wts" "sam_wts documentation"

end

subgraph Power

 sam_wts --> sam["sam_3d/sam_3dc"];

 style sam fill:#fcf
 click sam "https://megcore.nih.gov/index.php/Sam_3d_and_sam_3dc" "sam_3d/sam_3dc documentation"

end subgraph Connectivity

 sam_wts --> sam_power;
 style sam_power fill:#fcf
 click sam_power "https://megcore.nih.gov/index.php/Sam_power" "sam_power documentation"

end }}

Basic Task Based MEG Pipeline

In a task based analysis, you start with raw MEG data, as wells as data from the ADC channels - triggers, stimuli, and responses. Both of these must be pre-processed. Once your MEG data is marked appropriately, you can begin a SAM analysis. If you are interested in time-locked (evoked or event-related) signals, you can use either sam_4d or sam_4dc or sam_ers or sam_ersc, depending on exactly what you want as output. Alternatively, if you do not expect your signals to be time-locked, you can examine changes in induced power using sam_3d or sam_3dc.

{{#mermaid:graph LR

   MEG["MEG Data"] --> Filtering;

subgraph MEG PreProcessing

 Filtering --> Art["Artifact Removal"];

end

 ADC["ADC/Trigger Channels"] --> thresholdDetect;

subgraph ADC PreProcessing

 thresholdDetect --> add_markers;

end

subgraph SAM PreProcessing

 add_markers--> sam_cov;
 Art --> sam_cov;
 sam_cov --> sam_wts;
 style sam_cov fill:#fcf
 style sam_wts fill:#fcf
 click sam_cov "https://megcore.nih.gov/index.php/Sam_cov" "sam_cov documentation"
 click sam_wts "https://megcore.nih.gov/index.php/Sam_wts" "sam_wts documentation"

end

subgraph Induced Power

 sam_wts --> sam_3d["sam_3d/sam_3dc"];
 style sam_3d fill:#fcf
 click sam_3d "https://megcore.nih.gov/index.php/sam_3d_and_sam_3dc" "sam_3d/sam_3dc documentation"

end

subgraph Evoked/Event Related

 sam_wts --> sam_ers["sam_ers/sam_ersc"];
 sam_wts --> sam_4d["sam_4d/sam_4dc"];
 style sam_ers fill:#fcf
 click sam_ers "https://megcore.nih.gov/index.php/sam_ers_and_sam_ersc" "sam_ers/sam_ersc documentation"
 style sam_4d fill:#fcf
 click sam_4d "https://megcore.nih.gov/index.php/sam_4d_and_sam_4dc" "sam_4d/sam_4dc documentation"

end }}

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

MEG

   MEG["MEG Data"] --> sam_cov;

subgraph Phase I: Filter 20-70Hz

 sam_cov --> sam_wts;
 sam_wts --> sam_epi;
 style sam_cov fill:#fcf
 click sam_cov "https://megcore.nih.gov/index.php/Sam_cov" "sam_cov documentation"
 style sam_wts fill:#fcf
 click sam_wts "https://megcore.nih.gov/index.php/Sam_wts" "sam_wts documentation"

end

sam_epi --> NIFTIPeak["NIFTIPeak
Target
Identification"] NIFTIPeak --> sam_cov2["sam_cov"] style sam_epi fill:#fcf click sam_epi "https://megcore.nih.gov/index.php/sam_epi" "sam_epi documentation" style NIFTIPeak fill:#fcf click NIFTIPeak "https://megcore.nih.gov/index.php/NIFTIPeak" "NIFTIPeak.py documentation"

subgraph Phase II: Filter 1-150Hz

 sam_cov2 --> sam_wts2["sam_wts"]
 style sam_cov2 fill:#fcf
 click sam_cov2 "https://megcore.nih.gov/index.php/Sam_cov" "sam_cov documentation"
 style sam_wts2 fill:#fcf
 click sam_wts2 "https://megcore.nih.gov/index.php/Sam_wts" "sam_wts documentation"

end

 sam_wts2 --> DataEditor["DataEditor 
 Spike Identification"]

}}

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

 MRI["Structural MRI"] --> fids["Place Approximate 
 Fiducials"];

subgraph MRIproc

 fids --> FreeSurfer
 FreeSurfer --> FSNormals.py
 style FSNormals.py fill:#fcf
 click FSNormals.py "https://megcore.nih.gov/index.php/FSNormals.py" "FSNormals.py documentation"

end

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

subgraph MEGproc

 sam_cov-->sam_coreg
 sam_coreg--> patch_wts
 sam_coreg--> roi_wts
 sam_coreg--> sam_wts
 style sam_coreg fill:#fcf
 click sam_coreg "https://megcore.nih.gov/index.php/sam_coreg" "sam_coreg documentation"
 style patch_wts fill:#fcf
 click patch_wts "https://megcore.nih.gov/index.php/patch_wts" "patch_wts documentation"
 style roi_wts fill:#fcf
 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

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_3d documentation"
 style sam_4d fill:#fcf
 click sam_4d "https://megcore.nih.gov/index.php/sam_4d_and_sam_4dc" "sam_4d documentation"
 style sam_ers fill:#fcf
 click sam_ers "https://megcore.nih.gov/index.php/roi_wts" "sam_ers documentation"
 style sam_power fill:#fcf
 click sam_power "https://megcore.nih.gov/index.php/sam_power" "sam_power documentation"

end }}