Merge pull request #1508 from wiheto/master

[ENH] Include repetition time in functional summary

Author: oesteban

fmriprep/interfaces/reports.py

@@ -34,6 +34,7 @@
 
 FUNCTIONAL_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3>
 \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>Slice timing correction: {stc}</li>
 \t\t\t<li>Susceptibility distortion correction: {sdc}</li>
@@ -154,6 +155,7 @@ class FunctionalSummaryInputSpec(BaseInterfaceInputSpec):
                                    mandatory=True)
     output_spaces = traits.List(desc='Target spaces')
     confounds_file = File(exists=True, desc='Confounds file')
+    tr = traits.Float(desc='Repetition time', mandatory=True)
 
 
 class FunctionalSummary(SummaryInterface):
@@ -185,7 +187,7 @@ def _generate_segment(self):
         return FUNCTIONAL_TEMPLATE.format(
             pedir=pedir, stc=stc, sdc=self.inputs.distortion_correction, registration=reg,
             output_spaces=', '.join(self.inputs.output_spaces),
-            confounds=re.sub(r'[\t ]+', ', ', conflist))
+            confounds=re.sub(r'[\t ]+', ', ', conflist), tr=self.inputs.tr)
 
 
 class AboutSummaryInputSpec(BaseInterfaceInputSpec):

fmriprep/workflows/bold/base.py

@@ -361,7 +361,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                           slice_timing=run_stc,
                           registration='FreeSurfer' if freesurfer else 'FSL',
                           registration_dof=bold2t1w_dof,
-                          pe_direction=metadata.get("PhaseEncodingDirection")),
+                          pe_direction=metadata.get("PhaseEncodingDirection"),
+                          tr=metadata.get("RepetitionTime")),
         name='summary', mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
 
     func_derivatives_wf = init_func_derivatives_wf(output_dir=output_dir,