enh: finalize with plotting a report

nipreps · Dec 4, 2020 · 55adb11 · 55adb11
1 parent 6b4e72a
commit 55adb11
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diff --git a/dmriprep/config/reports-spec.yml b/dmriprep/config/reports-spec.yml
@@ -49,6 +49,23 @@ sections:
       all b=0 found in the dataset, after accounting for signal drift.
       The red contour shows the brain mask calculated using this reference b=0.
     subtitle: Reference b=0 and brain mask
+  - bids: {datatype: figures, desc: coreg, suffix: dwi}
+    caption: Diffusion-weighted data and anatomical data (EPI-space and T1w-space)
+      were aligned with <code>mri_coreg</code> (FreeSurfer).
+      WARNING - <code>bbregister</code> refinement rejected.
+    descriptions: Note that nearest-neighbor interpolation is used in this reportlet
+      in order to highlight potential slice Inhomogeneities and other artifacts, whereas
+      the final images are resampled using cubic B-Spline interpolation.
+    static: false
+    subtitle: Alignment of functional and anatomical MRI data (volume based)
+  - bids: {datatype: figures, desc: bbregister, suffix: dwi}
+    caption: Diffusion-weighted data and anatomical data (EPI-space and T1w-space)
+      were aligned with <code>bbregister</code> (FreeSurfer).
+    descriptions: Note that nearest-neighbor interpolation is used in this reportlet
+      in order to highlight potential slice Inhomogeneities and other artifacts, whereas
+      the final images are resampled using cubic B-Spline interpolation.
+    static: false
+    subtitle: Alignment of functional and anatomical MRI data (surface driven)
 - name: About
   reportlets:
   - bids: {datatype: figures, desc: about, suffix: T1w}
diff --git a/dmriprep/workflows/base.py b/dmriprep/workflows/base.py
@@ -362,11 +362,21 @@ def init_single_subject_wf(subject_id):
         t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")
 
         bbr_wf = init_bbreg_wf(
+            bold2t1w_dof=6,
             bold2t1w_init=config.workflow.dwi2t1w_init,
             omp_nthreads=config.nipype.omp_nthreads,
             use_bbr=True,
         )
 
+        ds_report_reg = pe.Node(
+            DerivativesDataSink(base_directory=str(output_dir), datatype="figures",),
+            name="ds_report_reg",
+            run_without_submitting=True,
+        )
+
+        def _bold_reg_suffix(fallback):
+            return "coreg" if fallback else "bbregister"
+
         # fmt:off
         workflow.connect([
             # T1w Mask
@@ -383,6 +393,9 @@ def init_single_subject_wf(subject_id):
             (anat_preproc_wf, bbr_wf, [
                 ("outputnode.fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm")
             ]),
+            (bbr_wf, ds_report_reg, [
+                ('outputnode.out_report', 'in_file'),
+                (('outputnode.fallback', _bold_reg_suffix), 'desc')]),
         ])
         # fmt:on