antsMultivariateTemplateConstruction2.sh repeats N4 on every iteration

[gdevenyi]

The location of the N4 code for template construction:
https://github.com/ANTsX/ANTs/blob/master/Scripts/antsMultivariateTemplateConstruction2.sh#L1490-L1492

Results in N4 being re-run on the input files for every iteration of the template construction. Computational time could be saved if it were moved to a step beforehand, or if a file check were added to see if the N4 processed files already exist.

[ntustison]

Thanks @gdevenyi . Do you want to put together a pull request or should I put it on my to-do list?

[gdevenyi]

If you agree this is worth addressing, I can do a PR.

Shall I check the other model scripts as well?

[ntustison]

Sure, as to the PR. But what model scripts are you referring to?

[gdevenyi]

Btp and antsMultivariateTemplateConstruction.sh

[ntustison]

Okay, sure.

[cookpa]

Thanks for this @ntustison and @gdevenyi

Should we also remove the default -b [ 200 ]? It will cause problems for non-human images.

[gdevenyi]

Should we also remove the default -b [ 200 ]? It will cause problems for non-human images.

I agree that's an issue, but I'm not sure what the default would do without that. In general the tools I write which wrap around ANTs, I usually calculate the largest physical scale of the image and start with that as the N4 distance.

[ntustison]

IMO, ideally we would remove N4 entirely from the template building scripts and simply leave it to the user to do any preprocessing. Outside of that, I agree with @gdevenyi in calculating it on the fly.

[cookpa]

OK I will leave it for now, and think more about how to prepare images in general.