Usage: imreg [options] base_image image_sequence ...
* Registers each 2D image in 'image_sequence' to 'base_image'.
* If 'base_image' = '+AVER', will compute the base image as
the average of the images in 'image_sequence'.
* If 'base_image' = '+count', will use the count-th image in the
sequence as the base image. Here, count is 1,2,3, ....
OUTPUT OPTIONS:
-nowrite Don't write outputs, just print progress reports.
-prefix pname The output files will be named in the format
-suffix sname 'pname.index.sname' where 'pname' and 'sname'
-start si are strings given by the first 2 options.
-step ss 'index' is a number, given by 'si+(i-1)*ss'
for the i-th output file, for i=1,2,...
*** Default pname = 'reg.'
*** Default sname = nothing at all
*** Default si = 1
*** Default ss = 1
-flim Write output in mrilib floating point format
(which can be converted to shorts using program ftosh).
*** Default is to write images in format of first
input file in the image_sequence.
-keepsize Preserve the original image size on output.
Default is without this option, and results
in images that are padded to be square.
-quiet Don't write progress report messages.
-debug Write lots of debugging output!
-dprefix dname Write files 'dname'.dx, 'dname'.dy, 'dname'.phi
for use in time series analysis.
ALIGNMENT ALGORITHMS:
-bilinear Uses bilinear interpolation during the iterative
adjustment procedure, rather than the default
bicubic interpolation. NOT RECOMMENDED!
-modes c f r Uses interpolation modes 'c', 'f', and 'r' during
the coarse, fine, and registration phases of the
algorithm, respectively. The modes can be selected
from 'bilinear', 'bicubic', and 'Fourier'. The
default is '-modes bicubic bicubic bicubic'.
-mlcF Equivalent to '-modes bilinear bicubic Fourier'.
-wtim filename Uses the image in 'filename' as a weighting factor
for each voxel (the larger the value the more
importance is given to that voxel).
-dfspace[:0] Uses the 'iterated diffential spatial' method to
align the images. The optional :0 indicates to
skip the iteration of the method, and to use the
simpler linear differential spatial alignment method.
ACCURACY: displacements of at most a few pixels.
*** This is the default method (without the :0).
-cmass Initialize the translation estimate by aligning
the centers of mass of the images.
N.B.: The reported shifts from the registration algorithm
do NOT include the shifts due to this initial step.
The new two options are used to play with the -dfspace algorithm,
which has a 'coarse' fit phase and a 'fine' fit phase:
-fine blur dxy dphi Set the 3 'fine' fit parameters:
blur = FWHM of image blur prior to registration,
in pixels [must be > 0];
dxy = convergence tolerance for translations,
in pixels;
dphi = convergence tolerance for rotations,
in degrees.
-nofine Turn off the 'fine' fit algorithm. By default, the
