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.. _ahelp_3dCM:

****
3dCM
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.. contents:: :local:


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    Usage: 3dCM [options] dset
    
    Output = center of mass of dataset, to stdout.
        Note: by default, the output is (x,y,z) values in RAI-DICOM
              coordinates.  But as of Dec, 2016, there are now
              command line switches for other options (see -local*
              below).
    
    
      -mask mset   :Means to use the dataset 'mset' as a mask:
                     Only voxels with nonzero values in 'mset'
                     will be averaged from 'dataset'.  Note
                     that the mask dataset and the input dataset
                     must have the same number of voxels.
    
      -automask    :Generate the mask automatically.
    
      -set x y z   :After computing the CM of the dataset, set the
                     origin fields in the header so that the CM
                     will be at (x,y,z) in DICOM coords.
    
      -local_ijk   :Output values as (i,j,k) in local orientation.
    
      -roi_vals v0 v1 v2 ... :Compute center of mass for each blob
                               with voxel value of v0, v1, v2, etc.
                               This option is handy for getting ROI 
                               centers of mass.
    
      -all_rois    :Don't bother listing the values of ROIs you want
                    the program will find all of them and produce a 
                    full list.
    
      -Icent :Compute Internal Center. For some shapes, the center can
              lie outside the shape. This option finds the location
              of the center of a voxel closest to the center of mass
              It will be the same or similar to a center of mass
              if the CM lies within the volume. It will lie necessarily
              on an edge voxel if the CMass lies outside the volume
    
      -Dcent :Compute Distance Center, i.e. the center of the voxel
              that has the shortest average distance to all the other
              voxels. This is much more computational expensive than
              Cmass or Icent centers
    
     -rep_xyz_orient RRR :when reporting (x,y,z) coordinates, use the
                    specified RRR orientation (def: RAI).
                    NB: this does not apply when using '-local_ijk',
                    and will not change the orientation of the dset
                    when using '-set ..'.