7.1.27. 2dImRegΒΆ

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++ 2dImReg: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2015) [64-bit] This program performs 2d image registration. Image alignment is performed on a slice-by-slice basis for the input 3d+time dataset, relative to a user specified base image.

** Note that the script @2dwarper.Allin can do similar things, ** ** with nonlinear (polynomial) warping on a slice-wise basis. **

Usage: 2dImReg

-input fname Filename of input 3d+time dataset to process

-basefile fname Filename of 3d+time dataset for base image
(default = current input dataset)
-base num Time index for base image (0 <= num)
(default: num = 3)
-nofine Deactivate fine fit phase of image registration
(default: fine fit is active)
-fine blur dxy dphi Set fine fit parameters
where:
blur = FWHM of blurring prior to registration (in pixels)
(default: blur = 1.0)
dxy = Convergence tolerance for translations (in pixels)
(default: dxy = 0.07)
dphi = Convergence tolerance for rotations (in degrees)
(default: dphi = 0.21)

-prefix pname Prefix name for output 3d+time dataset

-dprefix dname Write files ‘dname’.dx, ‘dname’.dy, ‘dname’.psi

containing the registration parameters for each slice in chronological order. File formats:

‘dname’.dx: time(sec) dx(pixels) ‘dname’.dy: time(sec) dy(pixels) ‘dname’.psi: time(sec) psi(degrees)

-dmm Change dx and dy output format from pixels to mm

-rprefix rname Write files ‘rname’.oldrms and ‘rname’.newrms

containing the volume RMS error for the original and the registered datasets, respectively. File formats:

‘rname’.oldrms: volume(number) rms_error ‘rname’.newrms: volume(number) rms_error

-debug Lots of additional output to screen

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