I am currently building a nipype workflow that involves segmentating T1w images using ANTs
Atropos. Relying on k-means for initialization can be unreliable because this is a macaque dataset, so I would like to use prior probability images instead (i.e.
-i PriorProbabilityImages). These images are warped from standard space to T1w-space via
The issue is that a string pattern is used to pass probability images to
Atropos, rather than a list of images (docs). So, in a workflow, there is actually no direct way you can pass in images to
I am wondering what the best way to go about this in a workflow. Would I have to manually fetch the working directory of the
antsApplyTransforms node and include it in the file string pattern? (Note that this may be complicated by the fact that the
antsApplyTransforms node is actually a MapNode that warps the 3 probability images, so all warped images aren’t in the same directory).