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 ..'.
