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ENH: Report number of echoes in BOLD summary. #2184

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Jun 9, 2020
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ENH: Report number of echoes in BOLD summary. #2184

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14 changes: 13 additions & 1 deletion fmriprep/interfaces/reports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
\t\t<ul class="elem-desc">
\t\t\t<li>Repetition time (TR): {tr:.03g}s</li>
\t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
\t\t\t<li>{multiecho}</li>
\t\t\t<li>Slice timing correction: {stc}</li>
\t\t\t<li>Susceptibility distortion correction: {sdc}</li>
\t\t\t<li>Registration: {registration}</li>
Expand Down Expand Up @@ -171,6 +172,7 @@ class FunctionalSummaryInputSpec(BaseInterfaceInputSpec):
tr = traits.Float(desc='Repetition time', mandatory=True)
dummy_scans = traits.Either(traits.Int(), None, desc='number of dummy scans specified by user')
algo_dummy_scans = traits.Int(desc='number of dummy scans determined by algorithm')
echo_idx = traits.List([], usedefault=True, desc="BIDS echo identifiers")


class FunctionalSummary(SummaryInterface):
Expand Down Expand Up @@ -218,10 +220,20 @@ def _generate_segment(self):
else:
dummy_scan_msg = dummy_scan_tmp.format(n_dum=self.inputs.algo_dummy_scans)

multiecho = "Single-echo EPI sequence."
n_echos = len(self.inputs.echo_idx)
if n_echos == 1:
multiecho = (
f"Multi-echo EPI sequence: only echo {self.inputs.echo_idx[0]} processed "
"in single-echo mode."
)
if n_echos > 2:
multiecho = (f"Multi-echo EPI sequence: {n_echos} echoes.")
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return FUNCTIONAL_TEMPLATE.format(
pedir=pedir, stc=stc, sdc=self.inputs.distortion_correction, registration=reg,
confounds=re.sub(r'[\t ]+', ', ', conflist), tr=self.inputs.tr,
dummy_scan_desc=dummy_scan_msg)
dummy_scan_desc=dummy_scan_msg, multiecho=multiecho)


class AboutSummaryInputSpec(BaseInterfaceInputSpec):
Expand Down
1 change: 1 addition & 0 deletions fmriprep/workflows/bold/base.py
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Expand Up @@ -267,6 +267,7 @@ def init_func_preproc_wf(bold_file):
registration_dof=config.workflow.bold2t1w_dof,
registration_init=config.workflow.bold2t1w_init,
pe_direction=metadata.get("PhaseEncodingDirection"),
echo_idx=echo_idxs,
tr=metadata.get("RepetitionTime")),
name='summary', mem_gb=config.DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
summary.inputs.dummy_scans = config.workflow.dummy_scans
Expand Down