Difference between revisions of "Source Localization - SAM"

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===== Synthetic Aperture Magnetometry =====
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=== Synthetic Magnetometry: The SAMsrcV3 Analysis Suite ===
  
The SAM software suite available here has been completely redesigned to incorporate numerous improvements in the analysis pipeline. Compared with older CTF tools, there are many new features (some of them experimental). Filtering options, more flexible control over active, control, and noise covariance matrices, dual-state imaging, realistic head models, and several flavors of multipole source imaging are available.
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The programs documented here implement the latest advances in MEG source localization. Compared with the older CTF tools, there are many new features (some of them experimental).  
  
There is also a new workflow resulting from a more efficient separation of functionality. All the new programs are named using a sam_ prefix, so there will be no confusion. The old CTF tools are normally installed in /opt/ctf, while the new programs are generally copied into a user's $HOME/bin directory.
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Features include:
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* Flexible control over active, control, and noise covariance matrices
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* Dual-state ERF imaging
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* Realistic head models
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* Hilbert envelope time series computation for connectivity
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* Experimental refinement of MRI coregistration based on Freesurfer normals
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* More efficient workflow
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* Command-line interface for maximal flexibility
  
* The latest source tarball is available here: [[local:/meg/SAMsrcV3-20170205.tgz|SAMsrcV3-20170205.tgz]].
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=== Documentation: ===
  
* Download and unpack:
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* [[SAMsrcV3 overview | SAMsrcV3 overview]]
 
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* [[Installation Instructions | Installation Instructions]]
: {| width=300 style="border: 1px solid lightgrey;"
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* [[Suggested Pipelines | Suggested Pipelines]]
|tar -xzvf SAMsrcV3-20170205.tgz
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* [[Tunable Parameters | Tunable Parameters]]
|}
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* SAM Program Reference Pages
 
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** [[sam_cov | sam_cov]]
* Examine the files in the config/ subdirectory, then run make. Binaries will be installed in the directory specified in the config/Makefile.config file, and defaults to the bin/ directory in the SAMsrcV3 directory. See also config/Makefile for a way to make symbolic links to a user's bin/ directory. Please contact [mailto:holroydt@mail.nih.gov Tom Holroyd]] if you need additional assistance with installation.
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** [[sam_coreg | sam_coreg]]
 
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** [[sam_wts | sam_wts]]
* Detailed documentation on the analysis suite is available [https://kurage.nimh.nih.gov/samdoc/  Here]
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** [[sam_nwts | sam_nwts]]
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** [[sam_3d and sam_3dc | sam_3d and sam_3dc]]
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** [[sam_4d and sam_4dc | sam_4d and sam_4dc]]
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** [[sam_ers and sam_ersc | sam_ers and sam_ersc]]
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** [[sam_power | sam_power]]
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** [[sam_epi | sam_epi]]
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** [[patch_wts | patch_wts]]
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** [[roi_wts | roi_wts]]
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** [[sam_entropy | sam_entropy]]
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** [[mut_img | mut_img]]
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* SAM Utility Program Reference Pages
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** [[orthohull.py | orthohull.py]]
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** [[FSnormals.py | FSnormals.py]]
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** [[NIFTIPeak | NIFTIPeak]]
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** [[3dNormalize | 3dNormalize]]

Latest revision as of 15:52, 30 September 2020

Synthetic Magnetometry: The SAMsrcV3 Analysis Suite

The programs documented here implement the latest advances in MEG source localization. Compared with the older CTF tools, there are many new features (some of them experimental).

Features include:

  • Flexible control over active, control, and noise covariance matrices
  • Dual-state ERF imaging
  • Realistic head models
  • Hilbert envelope time series computation for connectivity
  • Experimental refinement of MRI coregistration based on Freesurfer normals
  • More efficient workflow
  • Command-line interface for maximal flexibility

Documentation: