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feat: Switch to --force syn-sdc in comments, warnings and reports
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-4
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3 files changed

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fmriprep/data/reports-spec-func.yml

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@@ -78,7 +78,7 @@ sections:
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static: false
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subtitle: Susceptibility distortion correction
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- bids: {datatype: figures, desc: forcedsyn, suffix: bold}
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caption: The dataset contained some fieldmap information, but the argument <code>--force-syn</code>
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caption: The dataset contained some fieldmap information, but the argument <code>--force syn-sdc</code>
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was used. The higher-priority SDC method was used. Here, we show the results
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of performing SyN-based SDC on the EPI for comparison.
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static: false

fmriprep/data/reports-spec.yml

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@@ -104,7 +104,7 @@ sections:
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static: false
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subtitle: Susceptibility distortion correction
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- bids: {datatype: figures, desc: forcedsyn, suffix: bold}
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caption: The dataset contained some fieldmap information, but the argument <code>--force-syn</code>
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caption: The dataset contained some fieldmap information, but the argument <code>--force syn-sdc</code>
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was used. The higher-priority SDC method was used. Here, we show the results
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of performing SyN-based SDC on the EPI for comparison.
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static: false

fmriprep/workflows/base.py

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@@ -846,7 +846,7 @@ def map_fieldmap_estimation(
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# In the case where fieldmaps are ignored and `--use-syn-sdc` is requested,
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# SDCFlows `find_estimators` still receives a full layout (which includes the fmap modality)
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# and will not calculate fmapless schemes.
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# Similarly, if fieldmaps are ignored and `--force-syn` is requested,
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# Similarly, if fieldmaps are ignored and `--force syn-sdc` is requested,
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# `fmapless` should be set to True to ensure BOLD targets are found to be corrected.
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fmap_estimators = find_estimators(
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layout=layout,
@@ -870,7 +870,7 @@ def map_fieldmap_estimation(
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if ignore_fieldmaps and any(f.method == fm.EstimatorType.ANAT for f in fmap_estimators):
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config.loggers.workflow.info(
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'Option "--ignore fieldmaps" was set, but either "--use-syn-sdc" '
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'or "--force-syn" were given, so fieldmap-less estimation will be executed.'
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'or "--force syn-sdc" were given, so fieldmap-less estimation will be executed.'
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)
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fmap_estimators = [f for f in fmap_estimators if f.method == fm.EstimatorType.ANAT]
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