I’ve preprocessed data for several participants who have lesion masks. Unfortunately, the normalisation does not seem to be running well with the masks – the lesioned hemisphere seems to be bigger than the healthy one and is especially inflated around the lesion. I attach an example participant, this is the output in standard space MNI152NLin6Asym, it looks the same with the 2009 template and the same for the functional images.
Has anyone come accross this problem before? I assume other people have used fmriprep for data with lesion masks – did it work well for them? And does somebody know a solution to this?