[ENH] Give access to num_threads of N4BiasFieldCorrection #166
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Defaults to 1 (keep current behavior). N4BiasFieldCorrection is part of ANTs and the number of threads are controlled in the same way you'd do with antsRegistration.
niworkflows/anat/skullstrip.py
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| @@ -23,7 +23,8 @@ def afni_wf(name='AFNISkullStripWorkflow'): | |||
| outputnode = pe.Node(niu.IdentityInterface( | |||
| fields=['bias_corrected', 'out_file', 'out_mask', 'bias_image']), name='outputnode') | |||
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| inu_n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3, save_bias=True), | |||
| inu_n4 = pe.Node(ants.N4BiasFieldCorrection( | |||
| dimension=3, save_bias=True, num_threads=n4_nthreads), num_threads=n4_nthreads, | |||
| name='CorrectINU') | |||
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Node takes an n_procs parameter, not num_threads. Also PEP8 fix for white space:
inu_n4 = pe.Node(
ants.N4BiasFieldCorrection(dimension=3, save_bias=True, num_threads=n4_nthreads),
n_procs=n4_threads,
name='inu_n4')And should we be copying the header, as in fmriprep? Maybe it would make sense to move that here, and thread in the n4_threads?
niworkflows/anat/skullstrip.py
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| ants.N4BiasFieldCorrection(dimension=3, save_bias=True, num_threads=n4_nthreads), | ||
| n_procs=n4_nthreads, | ||
| name='inu_n4') | ||
| orig_hdr = pe.Node(CopyHeader(), name='orig_hdr') |
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orig_hdr has no in_file input.
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yes, just noticed (f57c315)
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Very prompt fix. |
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We could avoid issues like the above by pulling the whole |
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That would create a circular dependency between both. IMHO, the permanent solution to this would be to include the feature (with a proper boolean switch) in the |
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I read this as "moving" |
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Oh, ok, my bad. |
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Let's make it easier: nipy/nipype#2034 EDIT: I'll roll back this PR, so that it only works on the number of threads. |
Defaults to 1 (keep current behavior). N4BiasFieldCorrection is part
of ANTs and the number of threads are controlled in the same way you'd
do with antsRegistration.