Sam epi - Revision history

Nugenta: /* Description */

2019-03-12T15:46:46Z

Description

← Older revision		Revision as of 11:46, 12 March 2019
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	==Description==		==Description==

	The sam_epi routine is a program designed for detecting ~~sub-threshold~~ epileptiform activity in the brain. It evaluates each voxel ~~time~~ ~~series~~ to determine kurtosis. The recommended pipeline is to run sam_cov, sam_wts, and then sam_epi. The utility [[NIFTIPeak\|NIFTIPeak]] can then be used to identify voxels with peak or excess kurtosis values. These voxel locations can then be used as targets for a secondary run of sam_cov with a wide bandwidth, ~~an sam_wts~~. Finally, DataEditor can be used to generate the virtual sensor time series for the targets, and the epileptologist can investigate the time series ~~and~~ ~~mark~~ ~~spikes. Individual~~ spikes ~~can then be modeled with dipole fits~~.		The sam_epi routine is a program designed for detecting epileptiform activity in the brain in a semi-automated fashion, to prevent the necessity for the epileptologist to view each MEG channel time series individually. sam_epi evaluates the time series of each voxel in the brain to determine kurtosis. The recommended pipeline is to run sam_cov, sam_wts, and then sam_epi, using an initial bandwidth in the range 20-70Hz. The utility [[NIFTIPeak\|NIFTIPeak]] can then be used to identify voxels with peak or excess kurtosis values. These voxel locations can then be used as targets for a secondary run of sam_cov and sam_wts with a wide bandwidth (1-150Hz). Finally, DataEditor can be used to generate the virtual sensor time series for the targets, and the epileptologist can investigate the time series to examine individual spikes.

	Note that datasets must be continuous, and not epoched into trials.		Note that datasets must be continuous, and not epoched into trials.

	==Usage==		==Usage==

Nugenta at 15:13, 12 March 2019

2019-03-12T15:13:59Z

← Older revision		Revision as of 11:13, 12 March 2019
Line 3:		Line 3:
	==Description==		==Description==

	The sam_epi routine is a program designed for detecting sub-threshold epileptiform activity in the brain. It evaluates each voxel time series to determine kurtosis. The recommended pipeline is to run sam_cov, sam_wts, and then sam_epi. The utility [[NIFTIPeak\|NIFTIPeak]] can then be used to identify voxels with peak or excess kurtosis values. These voxel locations can then be used as targets for a secondary run of sam_wts.		The sam_epi routine is a program designed for detecting sub-threshold epileptiform activity in the brain. It evaluates each voxel time series to determine kurtosis. The recommended pipeline is to run sam_cov, sam_wts, and then sam_epi. The utility [[NIFTIPeak\|NIFTIPeak]] can then be used to identify voxels with peak or excess kurtosis values. These voxel locations can then be used as targets for a secondary run of sam_cov with a wide bandwidth, an sam_wts. Finally, DataEditor can be used to generate the virtual sensor time series for the targets, and the epileptologist can investigate the time series and mark spikes. Individual spikes can then be modeled with dipole fits.

	Note that datasets must be continuous, and not epoched into trials.		Note that datasets must be continuous, and not epoched into trials.

Nugenta: Created page with " Return to Source Localization - SAM ==Description== The sam_epi routine is a program designed for detecting sub-threshold epileptiform activi..."

2019-03-08T22:04:09Z

Created page with " Return to Source Localization - SAM ==Description== The sam_epi routine is a program designed for detecting sub-threshold epileptiform activi..."

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

==Description==

The sam_epi routine is a program designed for detecting sub-threshold epileptiform activity in the brain. It evaluates each voxel time series to determine kurtosis. The recommended pipeline is to run sam_cov, sam_wts, and then sam_epi. The utility [[NIFTIPeak|NIFTIPeak]] can then be used to identify voxels with peak or excess kurtosis values. These voxel locations can then be used as targets for a secondary run of sam_wts.

Note that datasets must be continuous, and not epoched into trials.

==Usage==

sam_epi -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:

CovBand: Bandpass for the covariance matrices (and directory for weights files)
ImageBand: Bandpass for the image
ImageMetric: Must be KURTOSIS
TimeInt: designates the duration for the boxcar integration
CovType: Must be GLOBAL

Optional Parameters:

FilterType: choose the applied filter, IIR vs. FFT
ImageDirectory: Directory where the output images are written, default is the SAM directory
PrefixLength: Number of characters in the MEG dataset name used for naming MRI files

==Output Files==

Creates a single 3D NIFTI format image of kurtosis (g2). Output file will be named using the PrefixLength parameter.