Difference between revisions of "Source Localization - SAM"

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


=== Synthetic Aperture Magnetometry ===
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.


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.
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.


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 For example, the old SAMsrc program has been replaced by a set of several new programs with a modern command-line interface.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.
* The latest source tarball is available here: [[:Media:SAMsrcV3-20170205.tgz|SAMsrcV3-20170205.tgz]].


Installation instructions:
* Download and unpack:

* The latest source tarball is available here: [[:Media:SAMsrcV3-20170205.tgz|SAMsrcV3-20170205.tgz]].


Download and unpack with:
: {| width=300 style="border: 1px solid lightgrey;"
|tar -xzvf SAMsrcV3-20170205.tgz
|}


tar -xzvf SAMsrcV3-20161215.tgz
* 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.


This will create a directory called SAMsrcV3.
* Detailed documentation on the analysis suite is available [https://kurage.nimh.nih.gov/samdoc/ Here]

Revision as of 14:43, 17 April 2018

The SAMsrcV3 MEG Analysis Suite

Synthetic Aperture Magnetometry

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.

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.

Installation instructions:

Download and unpack with:

tar -xzvf SAMsrcV3-20161215.tgz

This will create a directory called SAMsrcV3.