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: displacments 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
- algorithm is on, with parameters 1.0, 0.07, 0.21.