I have tried to create a bids pipeline containing only the pick_atlas-wf. I specified the inputs manually and did not connect the outputs of the pick_atlas-wf to anything.
It seems that Nipype skips important code of the relabel_atlas function (which is included in the pick_atlas-wf), when we don't connect the outputs of the pick_atlas-wf to anything.
Nipype probably doesn't recognise that we are saving something when we connect to our sinker (wf.connect(x, 'y', 'sinker', 'z') and since we are not using the results of the pick_atlas-wf, it skips important code.
I have tried to create a bids pipeline containing only the pick_atlas-wf. I specified the inputs manually and did not connect the outputs of the pick_atlas-wf to anything.
It seems that Nipype skips important code of the relabel_atlas function (which is included in the pick_atlas-wf), when we don't connect the outputs of the pick_atlas-wf to anything. Nipype probably doesn't recognise that we are saving something when we connect to our sinker (wf.connect(x, 'y', 'sinker', 'z') and since we are not using the results of the pick_atlas-wf, it skips important code.