Im using the following:
import nipype.interfaces.spm as spm
import nipype.pipeline engine as pe
infiles = [ ] # list containing directories to relevant niftii files
realigner = pe.Node(interface = spm.Realign(in_files = infile,
register_to_mean = True),
name = ‘realign’)
workflow = pe.Workflow(name = ‘preproc’)
workflow.base_dir = ‘.’
It seems to run but nothing seems to happen. I get the following in message:
171210-08:57:30,814 workflow INFO:
[‘check’, ‘execution’, ‘logging’]
171210-08:57:30,815 workflow INFO:
Process finished with exit code 0
Can you se what may be wrong here?
Nothing seems odd, you are running an empty workflow.
If you are going to run just one interface, maybe the
Workflow wrapping is an overkill.
Your code, with only interfaces:
realigner = spm.Realign(in_files=infile, register_to_mean=True)
result = realigner.run()
But, if you still want to use workflows (because you are building something bigger, or whatever other reason), then you’ll need to add the node into the workflow:
r_node = pe.Node(interface=spm.Realign(in_files=in_file, register_to_mean=True), name='realign')
workflow = pe.Workflow(name='preproc')
workflow.base_dir = os.getcwd()
When you call
workflow.connect([...connections...]) Nipype will call that
add_nodes() for you. But if you don’t call neither of them, the workflow remains empty and you were calling
run() on an empty workflow.