ENH: Mask multi-echo data with reference mask instead of echo-specific masks #2349
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I didn't realize that the bold_bold_trans_wf included the mask as an output too. Still need to select the first one, although the mask should be the same across echoes.
| (skullstrip_bold_wf, join_echos, [ | ||
| ('outputnode.skull_stripped_file', 'skullstripped_bold_files')]), | ||
| # use reference image mask used by bold_bold_trans_wf | ||
| (bold_bold_trans_wf, bold_t2s_wf, [ |
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I'd be careful to ensure that bold_bold_trans_wf does not depend on bold_t2s_wf. If this assumption is acceptable, then this seems the most reasonable solution to this problem.
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Is that because it would introduce a loop in the workflow? I agree that T2* mapping/optimal combination should happen after the native-space transforms are applied, mostly so that those transforms can be done all at once. There are solid reasons to do optimal combination after distortion correction, but I don't think that will have a very large effect on the data and I doubt that it's worth the extra effort since it would involve splitting up the transforms performed by bold_bold_trans_wf into two sets.
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Is that because it would introduce a loop in the workflow?
Yes, Nipype will not handle loops.
Co-authored-by: Oscar Esteban <code@oscaresteban.es>
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The failures seem like they're unrelated to the changes in this PR: _______________ ERROR collecting fmriprep/interfaces/__init__.py _______________
/src/fmriprep/fmriprep/interfaces/__init__.py:5: in <module>
from niworkflows.interfaces import (
/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/freesurfer.py:10: in <module>
from skimage import morphology as sim
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:121: in <module>
from ._shared import geometry
skimage/_shared/geometry.pyx:1: in init skimage._shared.geometry
???
E ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject |
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@tsalo could you rebase to see if the errors have been fixed? |
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Done! |
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@tsalo Quick bump to re-rebase. |
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@effigies done! |
Closes #2348.
Changes proposed in this pull request
bold_bold_trans_wfbefore callingbold_t2s_wf, use the reference image-based mask frombold_bold_trans_wf.bold_maskinput toinit_bold_t2s_wf.mask_fileinput toT2SMapinterface.Documentation that should be reviewed
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