Patch wts

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Under Construction

The purpose of patch_wts is to allow the user to calculate beamformer weights for extended patches of cortex define by the user, rather than being confined to the FreeSurfer parcellation, as in roi_wts. Similar to roi_wts, the position of the cortical normals can be used as the orientation of the sources. Note that this option should only be used if sam_coreg has been run. Alternatively, the user can request that the orientations remain unconstrained and are solved for in the typical fashion. ROIs are specified using a target file, giving not only a centroid coordinate, but also an extent. Also, like roi_wts, the activity from a patch of cortex is represented by a set of basis functions, likely resulting in a higher signal to noise than an analysis where the mean activity over the patch is calculated. Note that if a target file is not specified, the program will treat every voxel on the cortical surface as an individual patch. This would be very computationally intensive. Currently, weights are saved as NIFTI files, where the beamformer is only evaluated for voxels on the surface of the cortex. Future extensions of this program will utilize the GIFTI format instead.


 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
 -s  Solve for moment vector orientations (do not use cortical normals from FreeSurfer)

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

 CovBand: bandpass for covariance matrix calculation
 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 
 Model: Nolte is required. Other specifications will be ignored
 MRIDirectory: Specify where to locate the necessary MRI files (and target file)
 ImageStep: Specify output resolution 

Optional Parameters:

 Transform: Specifies transform written by sam_coreg
 PrefixLength: Specify characters used for identifying MRI and headmodel files.

Output Files

At this time, patch_wts outputs NIFTI images, where the 4th dimension encodes the channels. Note that only the voxels in immediate proximity to the cortical surface will be given. Future updates to the software will output GIFTI surface based files.