fix: make FieldmapReportlet accept 4D files

Author: oesteban

sdcflows/interfaces/reportlets.py

@@ -2,6 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Interfaces to generate speciality reportlets."""
 import numpy as np
+import nibabel as nb
 from nilearn.image import threshold_img, load_img
 from niworkflows import NIWORKFLOWS_LOG
 from niworkflows.viz.utils import cuts_from_bbox, compose_view
@@ -25,6 +26,7 @@ class _FieldmapReportletInputSpec(reporting.ReportCapableInputSpec):
                                  desc='a label name for the reference mosaic')
     moving_label = traits.Str('Fieldmap (Hz)', usedefault=True,
                               desc='a label name for the reference mosaic')
+    # pe_dir = traits.Enum(*tuple("ijk"), desc="PE direction")
 
 
 class FieldmapReportlet(reporting.ReportCapableInterface):
@@ -47,7 +49,13 @@ def _generate_report(self):
         NIWORKFLOWS_LOG.info('Generating visual report')
 
         movnii = refnii = load_img(self.inputs.reference)
-        fmapnii = load_img(self.inputs.fieldmap)
+        fmapnii = nb.squeeze_image(load_img(self.inputs.fieldmap))
+
+        if fmapnii.dataobj.ndim == 4:
+            for i, tstep in enumerate(nb.four_to_three(fmapnii)):
+                if np.any(np.asanyarray(tstep.dataobj) != 0):
+                    fmapnii = tstep
+                    break
 
         if isdefined(self.inputs.moving):
             movnii = load_img(self.inputs.moving)

sdcflows/models/tests/test_pepolar.py

@@ -46,8 +46,13 @@ def test_topup_wf(tmpdir, datadir, workdir, outdir, epi_path):
     # fmt: on
 
     if outdir:
+        from nipype.interfaces.afni import Automask
         from ...interfaces.reportlets import FieldmapReportlet
 
+        pre_mask = pe.Node(Automask(dilate=1, outputtype="NIFTI_GZ"),
+                           name="pre_mask")
+        merge_corrected = pe.Node(IntraModalMerge(hmc=False), name="merge_corrected")
+
         rep = pe.Node(
             FieldmapReportlet(reference_label="EPI Reference"), "simple_report"
         )
@@ -67,8 +72,11 @@ def test_topup_wf(tmpdir, datadir, workdir, outdir, epi_path):
 
         # fmt: off
         wf.connect([
-            (topup_wf, rep, [("outputnode.fieldmap", "fieldmap"),
-                             ("outputnode.corrected", "reference")]),
+            (topup_wf, pre_mask, [("outputnode.corrected", "in_file")]),
+            (topup_wf, merge_corrected, [("outputnode.corrected", "in_files")]),
+            (merge_corrected, rep, [("out_avg", "reference")]),
+            (topup_wf, rep, [("outputnode.fieldmap", "fieldmap")]),
+            (pre_mask, rep, [("out_file", "mask")]),
             (rep, ds_report, [("out_report", "in_file")]),
         ])
         # fmt: on