[RF] Split BOLD-T1w registration into calculation/application workflows #1278
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emdupre
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effigies
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Sep 13, 2018
fmriprep/workflows/bold/base.py
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| @@ -211,7 +211,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer, | |||
| * :py:func:`~fmriprep.workflows.bold.stc.init_bold_stc_wf` | |||
| * :py:func:`~fmriprep.workflows.bold.hmc.init_bold_hmc_wf` | |||
| * :py:func:`~fmriprep.workflows.bold.t2s.init_bold_t2s_wf` | |||
| * :py:func:`~fmriprep.workflows.bold.registration.init_bold_reg_wf` | |||
| * :py:func:`~fmriprep.workflows.bold.registration.init_bold_apply_reg_wf` | |||
| * :py:func:`~fmriprep.workflows.bold.registration.init_bold_calc_reg_wf` | |||
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For consistency, let's call the apply registration workflow and init_bold_t1_trans_wf. We could then go back to init_bold_reg_wf or init_bold_calc_reg_wf; either one.
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effigies
approved these changes
Sep 14, 2018
fmriprep/workflows/bold/base.py
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| ('t1_mask', 'inputnode.t1_mask'), | ||
| ('t1_aseg', 'inputnode.t1_aseg'), | ||
| ('t1_aparc', 'inputnode.t1_aparc')]), | ||
| (inputnode, bold_t1_trans_wf, [('bold_file', 'inputnode.name_source')]), |
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This should be merged with the previous (inputnode, bold_t1_trans_wf connection.
fmriprep/workflows/bold/base.py
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| (bold_t1_trans_wf, outputnode, [('outputnode.bold_aseg_t1', 'bold_aseg_t1'), | ||
| ('outputnode.bold_aparc_t1', 'bold_aparc_t1')]), | ||
| (bold_reg_wf, bold_t1_trans_wf, [ | ||
| ('outputnode.itk_bold_to_t1', 'inputnode.itk_bold_to_t1')]), |
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I would prefer this connection to go before the bold_t1_trans_wf -> outputnode one.
fmriprep/workflows/bold/base.py
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| ('outputnode.bold_aparc_t1', 'bold_aparc_t1')]), | ||
| (bold_reg_wf, bold_t1_trans_wf, [ | ||
| ('outputnode.itk_bold_to_t1', 'inputnode.itk_bold_to_t1')]), | ||
| (bold_t1_trans_wf, outputnode, [('outputnode.bold_t1', 'bold_t1')]), |
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Lets combine all of the (bold_t1_trans_wf, outputnode, connections.
effigies
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Changes proposed in this pull request
As discussed with @effigies, splits the existing
bold_reg_wfinto two separate, smaller workflows, one of which calculates the registrations and the other of which applies the result in a single-shot. This will make integration of ME-EPI workflow changes possible.Documentation that should be reviewed
Updated docstrings for both of the new functions.