ENH: Create fieldmap registration report

nipreps · Aug 30, 2023 · 4f6b565 · 4f6b565
1 parent 2a8abf5
commit 4f6b565
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Showing 2 changed files with 56 additions and 1 deletion.
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
@@ -349,7 +349,7 @@ def init_bold_fit_wf(
                 ])
                 # fmt:on
             else:
-                fmapreg_buffer.inputs.boldref2fmap_xform = boldref2fmap_xform
+                fmapreg_buffer.inputs.boldref2fmap_xfm = boldref2fmap_xform
 
             unwarp_wf = init_unwarp_wf(
                 free_mem=config.environment.free_mem,
@@ -380,6 +380,11 @@ def init_bold_fit_wf(
                 (unwarp_wf, regref_buffer, [
                     ('outputnode.corrected_mask', 'boldmask'),
                 ]),
+                (fmap_select, func_fit_reports_wf, [("fmap_ref", "inputnode.fmap_ref")]),
+                (fmapreg_buffer, func_fit_reports_wf, [
+                    ("boldref2fmap_xfm", "inputnode.boldref2fmap_xfm"),
+                ]),
+                (unwarp_wf, func_fit_reports_wf, [("outputnode.fieldmap", "inputnode.fieldmap")]),
             ])
             # fmt:on
         else:

diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
@@ -190,6 +190,7 @@ def init_func_fit_reports_wf(
     from niworkflows.interfaces.reportlets.registration import (
         SimpleBeforeAfterRPT as SimpleBeforeAfter,
     )
+    from sdcflows.interfaces.reportlets import FieldmapReportlet
 
     workflow = pe.Workflow(name=name)
 
@@ -198,9 +199,12 @@ def init_func_fit_reports_wf(
         "sdc_boldref",
         "coreg_boldref",
         "boldref2anat_xfm",
+        "boldref2fmap_xfm",
         "t1w_preproc",
         "t1w_mask",
         "t1w_dseg",
+        "fieldmap",
+        "fmap_ref",
         # May be missing
         "subject_id",
         "subjects_dir",
@@ -267,6 +271,40 @@ def init_func_fit_reports_wf(
     #       After: Resampled boldref with white matter mask
 
     if sdc_correction:
+        fmapref_boldref = pe.Node(
+            ApplyTransforms(
+                dimension=3,
+                default_value=0,
+                float=True,
+                invert_transform_flags=[True],
+                interpolation="LanczosWindowedSinc",
+            ),
+            name="fmapref_boldref",
+            mem_gb=1,
+        )
+
+        # SDC1
+        sdcreg_report = pe.Node(
+            FieldmapReportlet(
+                reference_label="BOLD reference",
+                moving_label="Fieldmap reference",
+                show="both",
+            ),
+            name="sdecreg_report",
+            mem_gb=0.1,
+        )
+
+        ds_sdcreg_report = pe.Node(
+            DerivativesDataSink(
+                base_directory=output_dir,
+                desc="sdcreg",
+                suffix="bold",
+                datatype="figures",
+                dismiss_entities=("echo",),
+            ),
+            name="ds_sdcreg_report",
+        )
+
         # SDC2
         sdc_report = pe.Node(
             SimpleBeforeAfter(
@@ -291,6 +329,18 @@ def init_func_fit_reports_wf(
 
         # fmt:off
         workflow.connect([
+            (inputnode, fmapref_boldref, [
+                ('fmap_ref', 'input_image'),
+                ('coreg_boldref', 'reference_image'),
+                ('boldref2fmap_xfm', 'transforms'),
+            ]),
+            (inputnode, sdcreg_report, [
+                ('sdc_boldref', 'reference'),
+                ('fieldmap', 'fieldmap')
+            ]),
+            (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]),
+            (inputnode, ds_sdcreg_report, [('source_file', 'source_file')]),
+            (sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]),
             (inputnode, sdc_report, [
                 ('sdc_boldref', 'before'),
                 ('coreg_boldref', 'after'),