Sam wts - Revision history

Nugenta at 19:35, 5 March 2019

2019-03-05T19:35:34Z

← Older revision		Revision as of 15:35, 5 March 2019
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	NumMarkers and MarkerN: Specify task markers		NumMarkers and MarkerN: Specify task markers
	ImageFormat: Specify Talairach or orig space weights		ImageFormat: Specify Talairach or orig space weights
			ImageBand: bandpass for weights


	Notes:		Notes:

Nugenta at 16:24, 5 March 2019

2019-03-05T16:24:51Z

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	Atlas: Specify use of a FreeSurfer surface atlas		Atlas: Specify use of a FreeSurfer surface atlas
	Transform: Specify a transform for the Atlas		Transform: Specify a transform for the Atlas
	Order: For realistic headmodel, specifies the order of the spherical harmonic expansion
	NumMarkers and MarkerN: Specify task markers		NumMarkers and MarkerN: Specify task markers
	ImageFormat: Specify Talairach or orig space weights		ImageFormat: Specify Talairach or orig space weights

Nugenta at 15:37, 5 March 2019

2019-03-05T15:37:18Z

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	Other options:		Other options:

	-v: Verbose mode, without this flag sam_wts works silently except for error messages		-v Verbose mode, without this flag sam_wts works silently except for error messages
	-Z: Normalize the SAM weights by the projected noise.		-Z Normalize the SAM weights by the projected noise.
	-B: Output forward solutions for a target list (along with the weights)		-B Output forward solutions for a target list (along with the weights)
	-h: Show help		-h Show help

	Required Parameters (in the .param file or on the command line):		Required Parameters (in the .param file or on the command line):

Nugenta at 15:36, 5 March 2019

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	-Z: Normalize the SAM weights by the projected noise.		-Z: Normalize the SAM weights by the projected noise.
	-B: Output forward solutions for a target list (along with the weights)		-B: Output forward solutions for a target list (along with the weights)
			-h: Show help

	Required Parameters:		Required Parameters (in the .param file or on the command line):
	Model: Specify the head model		Model: Specify the head model
	XBounds,YBounds,ZBounds,ImageStep or Atlas: Define the output coordinate space		XBounds,YBounds,ZBounds,ImageStep or Atlas: Define the output coordinate space

Nugenta at 15:32, 5 March 2019

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	==Usage==		==Usage==

	sam_wts -r <dataset_name> -m <parameter_file_name> ~~[-v]~~ [options]		sam_wts -r <dataset_name> -m <parameter_file_name> [options]

	The -r flag designates the dataset name (with or without the .ds suffix), -m designates the parameter file name~~, and -v is “verbose” mode. Without -v, sam_wts works silently, except for error messages~~.		The -r flag designates the dataset name (with or without the .ds suffix), and -m designates the parameter file name.

	Other options:		Other options:

			-v: Verbose mode, without this flag sam_wts works silently except for error messages
	-Z: Normalize the SAM weights by the projected noise.		-Z: Normalize the SAM weights by the projected noise.
	-B: Output forward solutions for a target list (along with the weights)		-B: Output forward solutions for a target list (along with the weights)

Nugenta at 19:20, 4 March 2019

2019-03-04T19:20:51Z

Show changes

Nugenta at 18:24, 4 March 2019

2019-03-04T18:24:13Z

← Older revision		Revision as of 14:24, 4 March 2019
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	[[Source Localization - SAM \| Return to Source Localization - SAM]]		[[Source Localization - SAM \| Return to Source Localization - SAM]]

			==Description==

			sam_wts computes linearly constrained minimum variance (LCMV) beamformer coefficients (SAM weights) for any designated ROI or target voxel list using the covariance files within the named dataset, calculated by [[sam_cov\|sam_cov]]. sam_wts is a scalar beamformer in which the optimal source dipole orientation is determined first, followed by computation of the scalar weights. Source orientation is estimated from a separate orientation covariance matrix (Orient.cov) that uses all data samples and a specified passband (ideally one in which signal-to-noise is optimal; see sam_cov). It is assumed that source orientation is stationary across time, whereas source amplitude may be non-stationary.

			In contrast to setting up a rectilinear grid by hand, an “atlas” file (created from a FreeSurfer parcellation) containing the position and orientation vectors of neocortical sources can be designated with the Atlas parameter. If the atlas file is present, the source grid (ROI and voxel spacing) is predetermined and the orientation estimate step is bypassed. In addition, the parameter file can designate a transform used to refine the translation and rotation of the atlas file. Generation of an atlas file requires FreeSurfer, [[FSnormals.py\|FSnormals.py]], and [[reduce_surface.py\|reduce_surface.py]]. If an atlas is specified, sam_wts will only solve for voxels that are immediate neighbors to the FreeSurfer surface, which will produce a sparse representation in a rectilinear voxel space.

			Three forward models are available for computing weights that are selectable using the Model parameter:

			*A single homogeneously conducting sphere, computed using the Sarvas equation.
			*Multiple local spheres, one per sensor, also computed with Sarvas.
			*A realistic head model (using the Nolte equations) computed
			with an estimate of the inner skull surface as determined by the AFNI program 3dSkullStrip.

			If desired, the covariance matrix can be regularized by adding a fixed noise value to its diagonal using the Mu or PropMu parameters. Regularization is in units of fT/\surdHz.

			Users who wish to develop real-time beamforming can also output a file containing the forward solutions for a small list of target locations using the -B option together with specifying a target file using the TargetName parameter (or -t).

			The output of sam_wts is a NIFTI file (number of voxels x number of sensors). In this format the SAM coefficients can be transformed to Talairach space by specifying ImageFormat TLRC RES (where RES is the grid spacing in millimetres) in the parameter file. This results in a second NIFTI file with a suffix of _at.nii, labeling it as @auto_tlrc output. If ImageFormat is absent, the weights default to the coordinates and grid spacing specified in the parameter ROI, as designated by XBounds, YBounds, ZBounds, and ImageStep. The user can also use ImageFormat ORIG, for which the output is .nii, only.

			Transformation of the SAM coefficients to Talairach space requires that the specified subject has an MRI that has been transformed to Talairach space. The recommended procedure is to run orthohull using the -t option on the subject’s anat+orig AFNI image file. This generates an image file named brain+tlrc that is read by the sam_wts program when ImageFormat TLRC is specified.

			The advantage of specifying Talairach space SAM weights is that subsequent analyses are automatically rendered in Talairach space for group studies. sam_wts calls the AFNI program @auto_tlrc, using nearest neighbor transformation (-rmode NN). In order to minimize the positional errors in Talairach space, it is recommended that ImageStep designates a finer grid spacing than the transformation. For example, a parameter file containing:

			XBounds 10 10
			YBounds -9 9
			ZBounds 0 15
			ImageStep .5
			ImageFormat TLRC 8.
			will compute SAM weights on a 5 mm grid and transform this to an 8 mm Talairach grid, using the nearest neighbors in ortho space for the corresponding weight in Talairach space.

			It’s also perfectly fine to run @auto_tlrc separately on the functional images produced by other SAM programs (such as sam_3d).

			==Usage==

			sam_wts -r <dataset_name> -m <parameter_file_name> [-v] [options]

			The -r flag designates the dataset name (with or without the .ds suffix), -m designates the parameter file name, and -v is “verbose” mode. Without -v, sam_wts works silently, except for error messages.

			Other options:

			-Z: Normalize the SAM weights by the projected noise.
			-B: Output forward solutions (used together with parameter “TargetName”).
			Parameters: The parameters specific to sam_wts include:

			NumMarkers
			Marker1
			Marker2 …
			Marker6
			XBounds
			YBounds
			ZBounds
			ImageStep
			MRIDirectory
			TargetName
			ImageFormat
			Atlas
			Transform
			Mu
			Model
			PrefixLength
			Example parameter file for a rectangular ROI in “ortho” space:

			NumMarkers 3
			Marker1 9r0 -.25 .25 TRUE
			Marker2 9r1 -.25 .25 TRUE
			Marker3 9r2 -.25 .25 TRUE
			CovBand 4 100
			ImageBand 35 45
			OrientBand 14 30
			XBounds -12 12
			YBounds -9 9
			ZBounds -2 15
			ImageStep .5
			Model Nolte
			Example parameter file using a cortical Atlas:

			NumMarkers 2
			Marker1 9r0 -.25 .25 TRUE
			Marker2 9r1 -.25 .25 TRUE
			CovBand 0 100
			ImageBand 14 30
			OrientBand 14 30
			Atlas example.mesh
			MRIDirectory WXYZABCD
			PrefixLength 8
			TargetName example_targets
			Model Nolte
			Input File Formats:

			Target File
			The named target file must be located in the subject’s MRI subdirectory (specified by the MRIDirectory and PrefixLength keywords). Each line has three numbers — the x, y, and z-coordinates in centimeters (separated by whitespace).
			Atlas File
			Each line has six numbers — the x, y, and z-coordinates (meters) and x, y, and z orientation (unit vector) (separated by whitespace).
			Notes
			The TargetName parameter takes precedence over the ROI specifications. If both are present, only the target list will be used. This directs sam_wts to compute legacy formatted weights in the dataset SAM subdirectory. The targets may be specified with or without the Atlas parameter.

			The target file used in the current version of SAM must not have the number of targets in the first line. Instead, each line contains the x, y, z coordinates (cm) separated by tabs or spaces and terminated by a newline character.

			Increasing the CovBand bandwidth is very useful for improving attenuation of strong interference such as from tDCS, tACS, and vagus nerve stimulators.

			DataEditor can be used to view the virtual sensor (source) time-series for a small number of target locations by reading its SAM weights. If the -Z flag is used to generate the weights, the units will be beamformer output signal-to-noise. Otherwise, the units are A-m.

			A target file can be generated by NIFTIPeak, which reads a SAM image file (.nii) and finds its local maxima. The maxima coordinates are output to a .max file in order of their magnitude. This file must be moved or copied to the subject’s MRI subdirectory.

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2019-03-04T17:45:00Z

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[[Source Localization - SAM | Return to Source Localization - SAM]]