Suggested Pipelines

Master Pipeline

{{#mermaid:graph LR

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

}}

Basic MRI Pre-Processing Workflow

{{#mermaid:graph LR subgraph MRI Preprocessing

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

{{#mermaid:graph LR

marks --> Covariance;

subgraph MEG Preprocessing

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

end

subgraph MEG Data Statistics

 meg --> Filter[Band-pass
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 }}

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