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ENH: Detect 3D BOLD series, warn and return empty workflow #2461

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merged 4 commits into from
Jul 20, 2021
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ENH: Detect 3D BOLD series, warn and return empty workflow #2461

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cd2caed
ENH: Detect 3D BOLD series, warn and return empty workflow
effigies Jul 19, 2021
c5227c1
Apply suggestions from code review
effigies Jul 19, 2021
d175f4f
Update fmriprep/workflows/bold/base.py
effigies Jul 19, 2021
11d9132
fix: too early to return a workflow
oesteban Jul 20, 2021
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10 changes: 9 additions & 1 deletion fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,15 @@ def init_func_preproc_wf(bold_file):
from niworkflows.interfaces.utils import DictMerge
from sdcflows.workflows.base import init_sdc_estimate_wf, fieldmap_wrangler

workflow = Workflow(name=wf_name)

if nb.load(bold_file).shape[3:] <= (1,):
config.loggers.workflow.warning(
f"3D BOLD series <{ref_file}> detected. Skipping."
)
return workflow


mem_gb = {'filesize': 1, 'resampled': 1, 'largemem': 1}
bold_tlen = 10

Expand Down Expand Up @@ -224,7 +233,6 @@ def init_func_preproc_wf(bold_file):
)

# Build workflow
workflow = Workflow(name=wf_name)
workflow.__postdesc__ = """\
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
Expand Down