Missing warp files in ANTs multivariate template construction for T1 and T2


Hi everyone, I’ve run into some trouble using antsMultivariateTemplateConstruction2.sh. This has previously been mention in another post by someone else (Ants Template Construction Warpfiles) which has not received any responses, which is why I was hoping to have more luck after posting this with a specific description of my problem.

To run the template building process have used the command:
antsMultivariateTemplateConstruction2.sh -d 3 -r 1 -k 2 -b 1 -c 2 -j 3 -o tmpl ids_tmplt.csv,
where the inputs are listed in a csv file in this format:

This produced very nice templates for both T1 and T2-weighted images. However, in the output directory, I now only find warp files for each subject for the T1 but not the T2 images. Also, when looking at the WarpedToTemplate images for each participant, the template and the individual participant’s images do not seem to align properly (as shown by the crosshairs in ITKsnap not being placed in the same position when viewing both images side by side). The log files look fine to me. The only note I get is “Your input image contains nonpositive values” with the original intensity range being [0, 664]. Does anyone know what is going on here and how I could fix it? That would be greatly appreciated!