FIX: Write out boldref-space brain mask with minimal level #3292
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Traveling so can't look closely, but does this avoid double-sinking in cases where boldref outputs are requested? |
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Ah good point. It doesn't yet, so I'll switch this to a draft until I've got everything working and there's no double-sinking. |
tsalo
commented
May 18, 2024
fmriprep/workflows/bold/outputs.py
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| ds_boldmask = pe.Node( | ||
| DerivativesDataSink( | ||
| base_directory=output_dir, | ||
| datatype='func', |
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I'm not sure if this is a good idea, but for some reason the files were written out to anat otherwise.
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I believe this will be fixed by passing in an original bold file.
effigies
reviewed
May 20, 2024
fmriprep/workflows/bold/fit.py
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| # fmt:off | ||
| workflow.connect([ | ||
| (hmcref_buffer, fmapref_buffer, [("boldref", "boldref_files")]), | ||
| (fmapref_buffer, enhance_boldref_wf, [("out", "inputnode.in_file")]), | ||
| (fmapref_buffer, ds_coreg_boldref_wf, [("out", "inputnode.source_files")]), | ||
| (ds_coreg_boldref_wf, regref_buffer, [("outputnode.boldref", "boldref")]), | ||
| (fmapref_buffer, ds_boldmask_wf, [("out", "inputnode.source_files")]), |
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Other workflows just set
ds_hmc_wf.inputs.inputnode.source_files = [bold_file]
I don't think I would worry about getting sbref vs bold straight here, as it's just a mask.
effigies
reviewed
May 20, 2024
effigies
approved these changes
May 20, 2024
effigies
added a commit
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Jun 4, 2024
23.2.3 (May 20, 2024) Bug fix release in the 23.2.x series. Writes brain masks in ``space-boldref`` with ``--level minimal``, bringing behavior in line with documentation. * FIX: Write out boldref-space brain mask with minimal level (#3292)
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Closes #3290.
Changes proposed in this pull request
init_ds_boldmask_wfworkflow. This might be overkill.init_bold_fit_wf.init_ds_bold_native_wf, since it's written out ininit_bold_fit_wfnow.