BIDSDataGrabber does not support derivatives domain

[jdkent]

Summary

The BIDSDataGrabber Interface cannot use the entities in the derivatives domain (as far as I can tell)

Actual behavior

If I point the BIDSDataGrabber Interface at a derivatives directory, none of the files are selected

Expected behavior

The BIDSDataGrabber interface should optionally use derivatives entities.

How to replicate the behavior

Point the BIDSDataGrabber interface at an fmriprep output directory as the base_dir.

Script/Workflow details

I patched the BIDSDataGrabber interface by adding a boolean for the input spec to specify derivatives and I added some logic and changed the call to the layout command to explicitly state which domains are to be used.

I can create a pull request if this is an actual issue.

Platform details:

{'commit_hash': '9f0ca09',
 'commit_source': 'repository',
 'networkx_version': '2.1',
 'nibabel_version': '2.2.1',
 'nipype_version': '1.1.7-dev+g9f0ca09',
 'numpy_version': '1.14.3',
 'pkg_path': '/media/Data/Documents/devel/nipype/nipype',
 'scipy_version': '1.1.0',
 'sys_executable': '/home/james/.conda/envs/atlascorr/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 19:16:44) \n'
                '[GCC 7.3.0]',
 'traits_version': '4.6.0'}

Execution environment

Choose one
-[x] My python environment outside container

[effigies]

I'm happy to see a PR. My only concern is maintaining backwards compatibility, so that upgrading nipype doesn't break somebody's pipeline. Though, with as unstable as pybids itself is, I'm not sure that's a valid concern...

[jdkent]

I checked to see how backwards compatible my change was. It didn't work on anything below version 0.6, I modified my code to change how the call was made depending on which version of pybids, since exclude was introduced in 0.5, I raised an error if the version of pybids was less than 0.5. You can find the changes on this pull request to another repository, I'll submit a pull request to nipype hopefully tomorrow.

But now that I think about it, the default for the 0.5 version is to include both bids and derivatives domains, so I may need to change the call to 0.5 again to maintain consistent behavior and only use the domains variable for versions > 0.6.