Hi, Philipp-
Well, I guess I asked for it... Silly me.
In the transformation_steps.jpg image you sent, is Panel A-left really a subject native space thing? It looks like a template.
Just to check about deobliquing, can you generate the following images:
@djunct_overlap_check \
-ulay orig_T1_UNI-DEN.nii.gz \
-olay MNI152_T1_1mm.nii.gz \
-prefix olap_t1_mni
and
@djunct_overlap_check \
-ulay target_native mtc.nii.gz \
-olay orig_T1_UNI-DEN.nii.gz \
-prefix olap_epi_t1
Each will likely make 2 images (one ignoring obliquity values, and one applying them), and it would be good to see both---because of a quirk of the MB underlying software, this might require 2 replies (because I think the most images that can be uploaded per post is 2).
Let's start there...
--pt
