Dealing with missing data in antsMultivariateTemplateConstruction2

[cauzzo-s5]

Dear experts
I'm using antsMultivariateTemplateConstruction2 to build a template from a dataset of T1 and T2FLAIR images.
My question is: Is it possible for the script to deal with missing images? For example, I have 60 subjects, all with a T1 but one subject does not have the T2. What is the best way to deal with this in your opinion?
Thank you

[ntustison]

Don't include that subject. A template made with 59 complete subjects will most likely be indistinguishable from a template made from 60 subjects.

[cauzzo-s5]

Thank you for your answer. After creation of the 59-subjects template, I would still like to have the T1 of my T2-missing subject registered to the template, making sure that this registration is as equivalent as possible to the registrations that have been computed by antsMultivariateTemplateConstruction2. In that way I would like to perform jacobian-based morphometry on the whole dataset.
I used "-d 3 -j 64 -i 8 -n 1 -k 2 -f 6x4x2x1 -r 1 -e 0 -b 1 -v 64gb -s 3x2x1x0 -q 100x100x70x20 -t BSplineSyN -m CC -c 5 " for antsMultivariateTemplateConstruction2.
How do I replicate that "-i" factor (which I assume imroves accuracy)? Should I simply concatenate 8 stages of antsRegistration with parameters "-d 3 -j 64 -n 1 -k 2 -f 6x4x2x1 -r 1 -e 0 -b 1 -v 64gb -s 3x2x1x0 -q 100x100x70x20 -t BSplineSyN -m CC -c 5 " ?

[ntustison]

There aren't 8 stages. -i 8 refers to the number of overall template building iterations and has nothing to do with each pairwise registration between the template and each subject. However, you should realize that if you want to have accurate mappings from each subject to the template, you have to follow up template building with mapping all subjects to the template.

[cookpa]

The template script updates the template after each registration, so the final output is registered to the previous template.

If things are working well, the template should converge and not change much. You can check this by looking at the intermediateTemplates/ directory.

The registration parameters used in each run should be in the job*.sh scripts, you can copy these and use them for your single-modality subject.