processing with phase/magnitude fmaps only

audreymhoughton commented 3 years ago

Errors I'm getting when I'm trying to run the pipeline with only 'magnitude1', 'magnitude2', 'phase1', and 'phase2' fieldmaps (I do not have epi fieldmaps I can use):

Traceback (most recent call last):
  File "/app/run.py", line 364, in <module>
    _cli()
  File "/app/run.py", line 67, in _cli
    return interface(**kwargs)
  File "/app/run.py", line 263, in interface
    session_spec = ParameterSettings(session, out_dir)
  File "/app/pipelines.py", line 147, in __init__
    types = self.bids_data['fmap'].keys()
AttributeError: 'list' object has no attribute 'keys'

This was noted while debugging that might help (ignore if they is not helpful):

helpers.py line 189: there needs to be cases added for magnitude/phase here

madisoth commented 3 years ago

A dataset I'm working on has magnitude1/magnitude2/phasediff (no phase1/phase2)-- if support for that combination can be added also, that would be a really huge help.

audreymhoughton commented 3 years ago

@madisoth phasediff is the difference between phase2 and phase1, right? Wouldn't that file have been created from phase1 and phase2 files to begin with? Or is phasediff acquired directly?

madisoth commented 3 years ago

I believe so, but this dataset doesn't include the original phase1/phase2, only phasediff.

audreymhoughton commented 3 years ago

@madisoth okay! @perronea and I have a time set up to look into adding phasediff capabilities in as well.

arueter1 commented 2 years ago

@madisoth will likely use a different pipeline to analyze these data. This enhancement is no longer needed.

DCAN-Labs / abcd-hcp-pipeline

processing with phase/magnitude fmaps only #32