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DOC: Better explain options #1358

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May 11, 2022
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DOC: Better explain options #1358

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29 changes: 18 additions & 11 deletions Scripts/antsMultivariateTemplateConstruction2.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -134,18 +134,25 @@ Optional arguments:
-w: Modality weights used in the similarity metric (default = 1): specified as
e.g. 1x0.5x0.75.

-q: Max iterations for each pairwise registration (default = 100x100x70x20):
specified in the form ...xJxKxL where
J = max iterations at coarsest resolution (here, reduced by power of 2^2)
K = middle resolution iterations (here, reduced by power of 2)
L = fine resolution iteratioxns (here, full resolution).
-q: Max iterations for each pairwise registration (default = 100x100x70x20): specified in
the form JxK...xF where
J = max iterations at first (coarsest) resolution
K = max iterations at next resolution
F = max iterations at the final resolution
Finer resolutions take much more time per iteration than coarser resolutions.

-f: Shrink factors (default = 6x4x2x1): Also in the same form as -q max iterations.
Needs to have the same number of components.

-s: Smoothing factors (default = 3x2x1x0): Also in the same form as -q max
iterations. Needs to have the same number of components.
The resolution for each level is controlled by the shrink factors "-f", so
"-q JxKxL -f 4x2x1" does J iterations at factor 4, K at factor 2, L at factor 1.

-f: Shrink factors in pairwise registration (default = 6x4x2x1): in the same form as "-q"
max iterations. Must have the same number of components as the iterations "-q" and smoothing
"-s". The shrink factors are integer factors for downsampling the the virtual space
(usually the template image) during registration.

-s: Smoothing kernels in pairwise registration (default = 3x2x1x0): also in the same form as
"-q" and "-f", with the same number of components. Standard deviation of a Gaussian smoothing
kernel applied to the images before downsampling at each level. Needs to have the same number
of components as the number of iterations and shrink factors. The kernel may be specified in
mm units or voxels with "AxBxCmm" or "AxBxCvox". Missing units implies vox.

-n: N4BiasFieldCorrection of moving image: 0 == off, 1 == on (default 1).

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