antsMultivariateTemplateConstruction2.sh default-value option

[tppm]

Operating system and version

Ubuntu

CPU architecture

x86_64 (PC, Intel Mac, other Intel/AMD)

ANTs code version

2.6.3

ANTs installation type

Downloaded Github release binaries

Summary of the problem

First of all, thank you for your work!

When making a template from CT images using antsMultivariateTemplateConstruction2.sh, the default padding value is 0, creating a grey border around the template. What is the best way to avoid this issue? Is there a way to specify a better default value for CT, like there is for registration? If not, I think this would be a great feature.

referring to issue #816, as it describes a similar issue, but with registration only.

Commands to reproduce the problem.

antsMultivariateTemplateConstruction2.sh

Output of the command with verbose output.

/

Data to reproduce the problem

/

[cookpa]

There isn't a way in the script, it would have to be edited such that the calls to antsApplyTransforms used the -f option.

Alternatively, you could shift the input intensities by a constant such that the average background is close to zero, then subtract that constant from the final template.