[RTM] Improved EPI skullstripping #519
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| (prepare_epi_opposite_wf, qwarp, [('outputnode.out_file', 'base_file')]), | ||
| ]) | ||
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| if usable_fieldmaps_matching_pe: | ||
| prepare_epi_matching_wf = init_prepare_epi_wf(ants_nthreads=ants_nthreads, | ||
| prepare_epi_matching_wf = init_prepare_epi_wf(ants_nthreads=omp_nthreads, |
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This is a fix of leftover variable, that should have been changed in the previous refactor.
fmriprep/workflows/util.py
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| outputnode = pe.Node(niu.IdentityInterface(fields=['mask_file', | ||
| 'skull_stripped_file', | ||
| 'bias_corrected_file', | ||
| 'reportlet']), |
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If we want to be consistent with usage, we generally call this out_report.
fmriprep/workflows/util.py
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| n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3), | ||
| name='n4_correct') | ||
| orig_hdr = pe.Node(CopyHeader(), name='orig_hdr') |
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Consider replacing n4_correct and orig_hdr with n4bias_wf. IMO it clarifies what's going on, as well as reduces lines of code and potential for errors.
fmriprep/workflows/util.py
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| @@ -8,13 +8,64 @@ | |||
| from __future__ import print_function, division, absolute_import, unicode_literals | |||
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| from nipype import logging | |||
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| LOGGER = logging.getLogger('workflow') | |||
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We don't actually use LOGGER anywhere in this file. Should we remove it, or keep it in case?
fmriprep/workflows/epi.py
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| ('t1_brain', 'fixed_image')]), | ||
| (gen_ref, mask_t1w_tfm, [('out_file', 'reference_image')]), | ||
| (fsl2itk_fwd, mask_t1w_tfm, [('itk_transform', 'transforms')]), | ||
| (mask_t1w_tfm, outputnode, [('output_image', 'epi_mask_t1')]), | ||
| (inputnode, mask_t1w_tfm, [('ref_epi_mask', 'input_image')]) |
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I'd prefer if this was in a block with the other inputs to mask_t1w_tfm.
chrisgorgo
changed the title
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This should be ready to go |
fmriprep/workflows/util.py
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| @@ -8,12 +8,59 @@ | |||
| from __future__ import print_function, division, absolute_import, unicode_literals | |||
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| from nipype import logging | |||
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Sorry, one last thing: Could you drop the logging import?
Since the workflow is built in docs, this can be a docs only commit, so we can fast track this.
Closes #515