:orphan: .. _ahelp_@ROI_decluster: ************** @ROI_decluster ************** .. contents:: :local: | Overview ======== .. code-block:: none Script to remove small clusters or standalone voxels from an ROI/atlas dataset Usage Example ============= .. code-block:: none @ROI_decluster \ -input mydset.nii.gz \ -outdir myoutdir \ -fracthresh 0.15 \ -prefix newroi_name Note only the input dataset and a threshold are required. Options ======= .. code-block:: none -input input_dset :required input dataset. This dataset should be set of integer values. The program mostly assumes approximate isotropic voxels. -outdir outdirname :directory name for output. All output goes to this directory. Default is roidc. -nvox_thresh nn :number of voxels in a cluster to keep -frac_thresh nn :fraction of voxels in a cluster to keep [0.0-1.0] Both types of threshold can be specified at the same time, in which case, the minimum value would be used. For example, an nvox_thresh of 10 and a frac_thresh of 0.15 would remove all voxels that occupied at least 15% of the number of voxels in the region and at least 10 voxels. -prefix baseprefix :base name of final output dataset, i.e. baseprefix.nii.gz Default is rdc, so output would be rdc.nii.gz -NN [1,2,3] :neighborhood type using in finding mode, 1 - facing neighbors, 2-edges, 3-corners Also see these programs with these related functions: 3dClusterize - reports and extracts clusters (main program called by this one) @ROI_modal_grow - grows regions using non-zero modal smoothing 3dROImaker - grows regions using regular dilation iteratively