Roi wts - Revision history

Nugenta at 20:36, 15 March 2019

2019-03-15T20:36:24Z

← Older revision		Revision as of 16:36, 15 March 2019
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	CovBand: bandpass for covariance matrix calculation		CovBand: bandpass for covariance matrix calculation
	Transform: ~~Must~~ be ~~TRUE~~		Transform: Specifies transform written by sam_coreg
	Atlas: Specifies the file containing the list of cortical normals in each ROI		Atlas: Specifies the file containing the list of cortical normals in each ROI
	ROIList: Specifies the file containing the list of ROIs to be estimated		ROIList: Specifies the file containing the list of ROIs to be estimated

Nugenta at 20:07, 15 March 2019

2019-03-15T20:07:07Z

← Older revision		Revision as of 16:07, 15 March 2019
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	The purpose of roi_wts is to leverage the orientation information from the FreeSurfer parcellation of the brain when solving for the beamformer weights. Normally, in a SAM analysis, the orientations calculated by solving the linear eigensystem equations and choosing the vector that gives the largest S/N. In roi_wts, the cortical normal vector is used instead. It is of paramount importance that the registration of the MEG and MRI are accurate. Thus, this program should only be run if you have already run sam_coreg. Obviously, one must have run FreeSurfer before running this program. This program also makes use of whatever parcellation that you have requested FreeSurfer use to annotate your surface.		The purpose of roi_wts is to leverage the orientation information from the FreeSurfer parcellation of the brain when solving for the beamformer weights. Normally, in a SAM analysis, the orientations calculated by solving the linear eigensystem equations and choosing the vector that gives the largest S/N. In roi_wts, the cortical normal vector is used instead. It is of paramount importance that the registration of the MEG and MRI are accurate. Thus, this program should only be run if you have already run sam_coreg. Obviously, one must have run FreeSurfer before running this program. This program also makes use of whatever parcellation that you have requested FreeSurfer use to annotate your surface.

	roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used.		roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used. This program represents the signal within the entire ROI using a set of basis functions, and is likely to produce greater signal to noise for the patch than a simple mean.

	==Usage==		==Usage==
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	Atlas: Specifies the file containing the list of cortical normals in each ROI		Atlas: Specifies the file containing the list of cortical normals in each ROI
	ROIList: Specifies the file containing the list of ROIs to be estimated		ROIList: Specifies the file containing the list of ROIs to be estimated
			Model: Nolte is required. Other specifications will be ignored.


	Optional Parameters:		Optional Parameters:

Nugenta at 17:40, 7 March 2019

2019-03-07T17:40:48Z

← Older revision		Revision as of 13:40, 7 March 2019
Line 6:		Line 6:

	roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used.		roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used.

			==Usage==

	roi_wts -r <dataset_name> -m <parameter_file_name> [options]		roi_wts -r <dataset_name> -m <parameter_file_name> [options]
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	CovBand: bandpass for covariance matrix calculation		CovBand: bandpass for covariance matrix calculation
	Transform: Must be TRUE		Transform: Must be TRUE
	Atlas: ~~specifies~~ the file		Atlas: Specifies the file containing the list of cortical normals in each ROI
			ROIList: Specifies the file containing the list of ROIs to be estimated

	Optional Parameters:		Optional Parameters:
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	MRIDirectory: Specify where to locate the necessary MRI files		MRIDirectory: Specify where to locate the necessary MRI files
	PrefixLength: Specify characters used for identifying MRI and headmodel files.		PrefixLength: Specify characters used for identifying MRI and headmodel files.

			==Output Files==

			roi_wts creates a log file, containing the rank, number of vertices used, source power, noise power, and s/n. In addition, a .nii file containing the weights is saved, such that there will be a single "voxel" in the X and Y directions, and the Z direction will encode the ROI. The tie dimension encodes the MEG Channels.

Nugenta at 15:18, 6 March 2019

2019-03-06T15:18:50Z

← Older revision		Revision as of 11:18, 6 March 2019
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	==Description==		==Description==

	The purpose of roi_wts is to leverage the orientation information from the FreeSurfer parcellation of the brain when solving for the beamformer weights. Normally, in a SAM analysis, the orientations calculated by solving the linear eigensystem equations and choosing the vector that gives the largest S/N. In roi_wts, the cortical normal vector is used instead. It is of paramount importance that the registration of the MEG and MRI are accurate. Thus, this program should only be run if you have already run sam_coreg. Obviously, one must have run FreeSurfer before running this program.		The purpose of roi_wts is to leverage the orientation information from the FreeSurfer parcellation of the brain when solving for the beamformer weights. Normally, in a SAM analysis, the orientations calculated by solving the linear eigensystem equations and choosing the vector that gives the largest S/N. In roi_wts, the cortical normal vector is used instead. It is of paramount importance that the registration of the MEG and MRI are accurate. Thus, this program should only be run if you have already run sam_coreg. Obviously, one must have run FreeSurfer before running this program. This program also makes use of whatever parcellation that you have requested FreeSurfer use to annotate your surface.

	roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used.		roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used.
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	Required Parameters (in the .param file or on the command line):		Required Parameters (in the .param file or on the command line):

			CovBand: bandpass for covariance matrix calculation
			Transform: Must be TRUE
			Atlas: specifies the file

	Optional Parameters:		Optional Parameters:

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2019-03-05T19:35:48Z

Created page with " Return to Source Localization - SAM ==Description== The purpose of roi_wts is to leverage the orientation information from the FreeSurfer par..."

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

==Description==

The purpose of roi_wts is to leverage the orientation information from the FreeSurfer parcellation of the brain when solving for the beamformer weights. Normally, in a SAM analysis, the orientations calculated by solving the linear eigensystem equations and choosing the vector that gives the largest S/N. In roi_wts, the cortical normal vector is used instead. It is of paramount importance that the registration of the MEG and MRI are accurate. Thus, this program should only be run if you have already run sam_coreg. Obviously, one must have run FreeSurfer before running this program.

roi_wts uses the Nolte (realistic) head model, and will ignore other specifications of the Model parameter. By default, a 20th order harmonic expansion of the hull is used.

roi_wts -r <dataset_name> -m <parameter_file_name> [options]

The -r flag designates the dataset name (with or without the .ds suffix), and -m designates the parameter file name.

Other options:

-v Verbose mode, without this flag sam_wts works silently except for error messages
-h Show help

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

Optional Parameters:

MRIDirectory: Specify where to locate the necessary MRI files
PrefixLength: Specify characters used for identifying MRI and headmodel files.