patchcorr3d(1)              General Commands Manual             patchcorr3d(1)

       patchcorr3d - Correlate a series of local patches from two volumes

       patchcorr3d xsize ysize zsize  nx ny nz  xlo xhi ylo yhi \
              zlo zhi filea fileb [transform_file original_fileb]

       patchcorr3d is a C-shell script that will determine the 3-D displace-
       ment between the two image volumes in filea and fileb, at a regular
       array of positions.  At each position, it extracts a patch from each of
       the two volumes using tapervoledge.  It then uses clip to do 3-D cross-
       correlation between the patches and determines the displacement of the
       patch in fileb relative to the patch in filea.

       The program outputs an initial line with the total number of patches,
       then one line for each patch, containing the X, Y, and Z coordinates of
       the patch and the displacement between the two files in X, Y, and Z.

       The size of the patches in X, Y, and Z is set by the arguments xsize,
       ysize, and zsize.

       The number of patches in X, Y, and Z is set by the arguments nx, ny,
       and nz.

       The lower and upper limits of the region from which patches will be
       extracted are set by xlo and xhi in X, ylo and  yhi in Y, and zlo and
       zhi in Z.

       In addition, the region can be limited further if fileb was transformed
       from an original volume and appreciably shifted by that transformation.
       If the optional arguments transform_file and original_fileb are
       included, then the limits of the region for patches will be adjusted to
       exclude domains in fileb that back-transform to coordinates outside the
       bounds of the original fileb.

       David Mastronarde  <mast at colorado dot edu>

       tapervoledge, clip

IMOD                                4.11.0                      patchcorr3d(1)