Realign

_images/realign.png
  • Estimate: Estimate parameters for realignment.
    • quality: Highest quality (1) gives most precise results, whereas lower qualities gives faster realignment.
    • sep: The separation (in mm) between the points sampled in the reference image. Smaller sampling distances gives more accurate results, but will be slower.
    • fwhm: Full width at half maximum of the Gauss smoothing kernel (mm).
    • rtm: 1 indicates images are registered to the mean image, while 0 indicates images are registered to the first image in each subject’s folder.
    • wrap: 3 dimensions of wrapping, e.g. [1 1 1] for wrapping in X, Y and Z direction, [0 0 0] for no wrapping.
    • interp: Indexes of interpolation methods. (1 for Trilinear; 2-7 for 2nd-7th Degree B-Spline).
  • Write:
    • which: The first parameter allows 0, 1 and 2 as input (0: create only a mean resliced image; 1: don’t reslice the first image. 2: reslice all the image). The second parameter indicates whether to output a resliced mean image (0 for false and nonzero for true).
    • interp: Interpolation methods for write option. (0 for Nearest Neighbor; 1 for Trilinear; 2-7 for 2nd-7th Degree B-Spline; Inf for Fourier Interpolation).
    • mask: Mask output images (true/false). If any image has a zero value at a voxel, then all images will have zero (or NaNs if allowed) values at that voxel.
    • wrap: 3 dimensions of wrapping, e.g. [1 1 1] for wrapping in X, Y and Z direction, [0 0 0] for no wrapping.
    • prefix: Output images will have a prefix of r by default.
  • Reference: spm manual.