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compute_warp - Compute non-linear warp field of 2 MRI's  

1997 Ulrik Kjems, DSP/IMM, Technical University of Denmark, uk@imm.dtu.dk
Use : 
  compute_warp [-h] | [optionsfile {keyword=value}]

Compute an invertible deformation which warps one image (data) volume to look
like a template. The inverse ('reconciled') mapping is computed as well.
The deformation is represented as a volume of displacement vectors
sampled over the volumes field of view, but in a lower resolution.

The optionsfile contains the parameters for the warp. If '-' is specified
as optionsfile, no options are read.
The optionsfile is an ASCII file, each line assigns a value or a list of 
values to a keyword. Anything after '#' on a line is ignored.

keyword = value {value}
# comments after the garden-gate

Recognized keywords are:

Keyword		Single/List,Type	Description
-----------------------------------------------------------------------------
outfileformat,fileformat,outputfileformat:
			S,%d	Default output file format (see volio.h), 0
				(def) same as template, 2=VAPET, 3=ANALYZE
basedir			S,%s	Base directory to prepend all file names
templatefiles,templatefile:
			S,%s	Volume to use as target for warp
datafiles,datafile	S,%s	Volume to use as subject for warp
outfile_warped,outfile_inv_warped,outfile:
			S,%s	Warped subject volume (not computed if not
				specified)
outfile_field		S,%s	Volume of computed displacement field
				template-to-data (X, Y and Z components in
				cm's)
outfile_inv_field	S,%s	Volume of computed inverse displacement field,
				data-to-template (X, Y and Z components in
				cm's)
logfile			S,%s	File to log all output
dumpfile		S,%s	File to log all convergence data. Useful for
				estimating the parameters and monitor
				convergence. 
sig_level,debug_level,level,signal_level:
			S,%s	Control of chat level ('silent', 'std', 'info',
				'debug')
method			L,%d	Cost function for warp: 0: least square, 1:
				squared scaled, 2: local mean subtractred least
				squares, 3: max mutual information 4: min.
				entropy, 5: correlation coefficient.
no_reconcile		S,%d	Set to nonzero to disable warp reconcilation
				procedure (reconcile is default)
auto,autoregularize,autoreg:
			L,%d	Set to 1 for automated regularization (auto set
				alpha, default off)
alpha			L,%f	Parameter to constrain warp: neighborhood
				connection
gamma_d			S,%f	Truncation filtering D (no need to set)
d_filter_fwhm		L,%f	Smoothness enforcer: FWHM of Gauss used for
				filtering displacement map.
search			L,%d	Size of local search regions in voxels
segx			L,%d	Segmentation size X
segy			L,%d	       -          Y
segz			L,%d	       -          Z
resx			L,%d	Working resolution X
resy			L,%d	       -           Y
resz			L,%d	       -           Z
repeat,iterations,max_repeat:
			L,%d	Max. number of iteration repeats at same
				parameter settings
min_rel_change		S,%f	Min. rel change in cost function when doing
				repeated iterations with constant parameter
				settings
dump_cf			L,%d	Dump CF file (debug opt.)
dump_cnvar		L,%d	Dump neighborhood variance volume CNVAR file
				(debug opt.)
dump_cmvar		L,%d	Dump match variance volume CMVAR file (debug
				opt.)
compute_warp -h produces above information

Ulrik Kjems
6/3/1998