## Note: This page was created with the CommandTemplate ## ## If you're modifying this page please take a look at the ## latest version of CommandTemplate to ensure that you're ## using the latest version of the CommandTemplate ## ## See HelpOnCommandTemplate for description of formatting '''Index''' <> = Name = mri_nl_align - pairwise non-linear warp between two 3D volumes = Synopsis = mri_nl_align [-view x y z] [-w k] [-z ] [-sigma ] [-dt ] [-intensity l_log_likelihood] [-T initial transformation] = Arguments = == Positional Arguments == || || FIXED volume || volume to which the second argument gets warped || || || MOVING volume || volume that gets warped to thefirst argument || || || registration output || the warp that aligns the moving volume to the fixed one || == Optional Flagged Arguments == || -view x y z || brief description ||detailed description (eg, help file information) || || -w k || write iterations || write an mgz volume and 3 orthogonal views (.tif) at each k^th iteration || || -z || disabling zero image locations || || || -sigma || || || || -dt || || || || -intensity l_log_likelihood || || || || -T transform || initial transformation || || = Outputs = || || the resulting non-linear registration warp || = Description = Non-linear volumetric registration between two input volumes. Suited to align mono-modal images as the objective function is SSE. = Examples = == Example 1 == command foo -i f -o out description == Example 2 == command foo -i f -o out -f fvalue description = Bugs = None = See Also = [[othercommand1]], [[othercommand2]] = Links = FreeSurfer, FsFast = Methods Description = {{{ description description }}} = References = [[References/Lastname###]] = Reporting Bugs = Report bugs to = Author/s = BruceFischl