From 9ae645c362dd501c96b5daf624eeadcf42b58009 Mon Sep 17 00:00:00 2001 From: Philip Cook Date: Tue, 10 May 2022 17:07:13 -0400 Subject: [PATCH] DOC: Better explain options --- .../antsMultivariateTemplateConstruction2.sh | 29 ++++++++++++------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/Scripts/antsMultivariateTemplateConstruction2.sh b/Scripts/antsMultivariateTemplateConstruction2.sh index 7be9cc955..e50e9a5ca 100755 --- a/Scripts/antsMultivariateTemplateConstruction2.sh +++ b/Scripts/antsMultivariateTemplateConstruction2.sh @@ -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).