Transformix (ApplyWarp()) doesn't generate output

Hi everyone!

I am using Nipype for a preprocessing pipeline. In my pipeline I use transformix (function ApplyWarp() from the elastix interface).

When I apply the ApplyWarp() function seperately and use ApplyWarp().run, it works perfectly.
However, when I use the function inside a Node in the pipeline, the node executes but the warped_file of the output is never generated. I cannot find a ‘result.nii’ file anywhere.

How could I fix this?


You want to set remove_unnecessary_outputs to false in the config file. Please check out this tutorial.