SAMentropy Version 3

Description: SAMentropy computes the rank vector entropy (RVE) for continuous data and outputs a 3D+time image. It does not compute event-related RVE (for which see, SAM3d/SAM3dc, SAM4d/SAM4dc, or SAMers/SAMersc). SAMentropy is intended for use in connectivity studies of the correlation of the envelope of power among voxels -- e.g., by using ICA or the AFNI, function "Instacorr".

SAMentropy applies the beamformer coefficients to the filtered MEG data (specified by ImageBand) to compute the estimated source time-series. It then transforms the voxel time series to a rank vector entropy time-series for an embedding space of 4 or 5 dimensions to obtain the envelope of power. This is written to the corresponding voxel.

Usage:

SAMentropy -r <dataset_name> -m <parameter_file_name> -v

The -r flag is followed by the dataset name (with or without the .ds suffix). The -m flag is followed by the parameter file name without the .param suffix. The -v argument specifies verbose output — else SAMentropy works silently.

Optional flags are:

The required parameter file keywords for SAMentropy are:

Optional keywords include:

Example parameters for imaging rank vector entropy for broad-band activity (4-150 Hz) in a 4-dimensional embedding space, in Taliarach space on an 8mm grid:

NumMarkers 0
CovBand 4.0 150.0
ImageBand 4.0 150.0
XBounds -12 12
YBounds -9 9
ZBounds -2 15
ImageStep 0.5
ImageFormat TLRC 8.0
Mask /data2/Mask8mm.nii
ImageMetric RankVectorEntropy 0.5 4
CovType GLOBAL
MRIDirectory /data1/mri
ImageDirectory /data1/Rest/Images
TimeStep 0.01
BaselineRemoval BYVOXEL