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== The SAMsrcV3 MEG Analysis Suite ==
=== 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).
=== Synthetic Aperture Magnetometry ===


Features include:
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). True within-subject statistics are now available, including a non-parametric test in addition to the usual t and F tests. There is much better handling of shorter time windows, a more flexible control over active, control, and noise covariance matrices, dual-state ERF imaging, realistic head models, and several flavors of multipole source imaging that are available, though some of these latter features are still considered experimental.
* 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: ===
There is also a new work flow resulting from a more efficient separation of functionality. For example, the old SAMsrc program has been replaced by a set of several new programs with a modern command-line interface. The old CTF tools were normally installed in /opt/ctf. The new set of programs will generally be copied into a user’s $HOME/bin directory. Many of the old tools are still useful and necessary.


* [[SAMsrcV3 overview | SAMsrcV3 overview]]
A wiki containing documentation for the SAM suite is [https://kurage.nimh.nih.gov/samdoc/ here]. It's still a work in progress.
* [[Installation Instructions | Installation Instructions]]

* [[Suggested Pipelines | Suggested Pipelines]]
'''Installation instructions:'''
* [[Tunable Parameters | Tunable Parameters]]

* SAM Program Reference Pages
Linux system (tested under CentOS 6.x, CentOS 7.x, Ubuntu 14.04 LTS, Ubuntu 16.04 LTS, Fedora 27)
** [[sam_cov | sam_cov]]
The latest source tarball is available here: [[:Media:SAMsrcV3-20170205.tgz|SAMsrcV3-20170205.tgz]].
** [[sam_coreg | sam_coreg]]
Download and unpack with:
** [[sam_wts | sam_wts]]
tar -xzvf SAMsrcV3-20170205.tgz
** [[sam_nwts | sam_nwts]]

** [[sam_3d and sam_3dc | sam_3d and sam_3dc]]
MacOS Users using the '''clang''' compiler (tested under macOS 10.13.x)
** [[sam_4d and sam_4dc | sam_4d and sam_4dc]]
The latest source tarball is available here: [[:Media:SAMsrcV3-20170205_clang.tgz|SAMsrcV3-20170205_clang.tgz]].
** [[sam_ers and sam_ersc | sam_ers and sam_ersc]]
Download and unpack with:
** [[sam_power | sam_power]]
tar -xzvf SAMsrcV3-20170205_clang.tgz
** [[sam_epi | sam_epi]]

** [[patch_wts | patch_wts]]
MacOS Users using the '''gcc-7''' compiler (tested under macOS 10.13.x)
** [[roi_wts | roi_wts]]
The latest source tarball is available here: [[:Media:SAMsrcV3-20170205_gcc-7.tgz|SAMsrcV3-20170205_gcc-7.tgz]].
** [[sam_entropy | sam_entropy]]
Download and unpack with:
** [[mut_img | mut_img]]
tar -xzvf SAMsrcV3-20170205_gcc-7.tgz
* SAM Utility Program Reference Pages

** [[orthohull.py | orthohull.py]]
This will create a directory called SAMsrcV3.
** [[FSnormals.py | FSnormals.py]]
** [[NIFTIPeak | NIFTIPeak]]
** [[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:

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