enh: add background mosaic

mriqc/data/bootstrap-dwi.yml

@@ -31,11 +31,6 @@ sections:
 - name: Summary
   reportlets:
   - bids: {datatype: figures, desc: summary, extension: [.html]}
-  - bids: {datatype: figures, desc: background}
-    caption: This panel shows a mosaic enhancing the background around the head.
-      Artifacts usually unveil themselves in the air surrounding the head, where no signal
-      sources are present.
-    subtitle: View of the background of the voxel-wise average of the DWI orientations
 - name: DWI shells
   ordering: bval
   reportlets:
@@ -51,50 +46,11 @@ sections:
       such as those intrinsic to SMS parallelization.
     subtitle: Voxel-wise standard deviation calculated across volumes in this <em>DWI shell</em>,
       zoomed-in covering just the brain
-- name: Extended visual report
-  reportlets:
   - bids: {datatype: figures, desc: background}
     caption: This panel shows a mosaic enhancing the background around the head.
       Artifacts usually unveil themselves in the air surrounding the head, where no signal
       sources are present.
-    subtitle: View of the background of the voxel-wise average of the BOLD timeseries
-  - bids: {datatype: figures, desc: mean}
-    subtitle: Average signal through time
-    caption: The average signal calculated across the last axis (time).
-  - bids: {datatype: figures, desc: airmask}
-    caption: The <em>hat</em>-mask calculated internally by MRIQC. Some metrics will use this
-      mask, for instance, to find out artifacts and estimate the spread of gaussian noise
-      added to the signal. This mask leaves out the air around the face to avoid measuring
-      noise sourcing from the eyeballs and their movement.
-    subtitle: '&laquo;Hat&raquo;-mask'
-  - bids: {datatype: figures, desc: noisefit}
-    caption: The noise fit internally estimated by MRIQC to calculate the QI<sub>1</sub> index
-      proposed by <a href="https://doi.org/10.1002/mrm.21992" target="_blank">Mortamet et al. (2009)</a>.
-    subtitle: Distribution of the noise within the <em>hat</em> mask
-    style:
-      max-width: 450px
-  - bids: {datatype: figures, desc: artifacts}
-    caption: Mask of artifactual intensities identified within the <em>hat</em>-mask.
-    subtitle: Artifactual intensities on the background
-  - bids: {datatype: figures, desc: brainmask}
-    caption: Brain mask as internally extracted by MRIQC. Defects on the brainmask could
-      indicate problematic aspects of the image quality-wise.
-    subtitle: Brain extraction performance
-  - bids: {datatype: figures, desc: head}
-    caption: A mask of the head calculated internally by MRIQC.
-    subtitle: Head mask
-  - bids: {datatype: figures, desc: segmentation}
-    caption: Brain tissue segmentation, as internally extracted by MRIQC.
-      Defects on this segmentation, as well as noisy tissue labels could
-      indicate problematic aspects of the image quality-wise.
-    subtitle: Brain tissue segmentation
-  - bids: {datatype: figures, desc: norm}
-    caption: This panel shows a <em>quick-and-dirty</em> nonlinear registration into
-      the <code>MNI152NLin2009cAsym</code> template accessed with
-      <a href="https://templateflow.org/browse" target="_blank"><em>TemplateFlow</em></a>.
-    subtitle: Spatial normalization of the anatomical image
-    static: false
-
+    subtitle: View of the background of the voxel-wise average of this <em>DWI shell</em>
 
 - name: About
   nested: true

mriqc/reports/individual.py

@@ -78,7 +78,7 @@ def _single_report(in_file):
     prov["Versions_TemplateFlow"] = config.environment.templateflow_version
 
     bids_meta = config.execution.layout.get_file(in_file).get_metadata()
-    bids_meta.pop("global")
+    bids_meta.pop("global", None)
 
     robj = Report(
         config.execution.output_dir,

mriqc/workflows/diffusion/output.py

@@ -96,12 +96,13 @@ def init_dwi_report_wf(name="dwi_report_wf"):
         iterfield=["in_file"],
     )
 
-    mosaic_noise = pe.Node(
+    mosaic_noise = pe.MapNode(
         PlotMosaic(
             only_noise=True,
             cmap="viridis_r",
         ),
-        name="PlotMosaicNoise",
+        name="mosaic_noise",
+        iterfield=["in_file"],
     )
 
     if config.workflow.species.lower() in ("rat", "mouse"):
@@ -134,6 +135,18 @@ def init_dwi_report_wf(name="dwi_report_wf"):
         iterfield=["in_file", "bval"],
     )
 
+    ds_report_noise = pe.MapNode(
+        DerivativesDataSink(
+            base_directory=reportlets_dir,
+            desc="background",
+            datatype="figures",
+            allowed_entities=("bval",),
+        ),
+        name="ds_report_noise",
+        run_without_submitting=True,
+        iterfield=["in_file", "bval"],
+    )
+
     def _gen_entity(inlist):
         return ["00000"] + [f"{int(round(bval, 0)):05d}" for bval in inlist]
 
@@ -143,12 +156,16 @@ def _gen_entity(inlist):
                                   ("brainmask", "bbox_mask_file")]),
         (inputnode, mosaic_stddev, [("in_stdmap", "in_file"),
                                     ("brainmask", "bbox_mask_file")]),
+        (inputnode, mosaic_noise, [("in_avgmap", "in_file")]),
         (inputnode, ds_report_mean, [("name_source", "source_file"),
                                      (("in_shells", _gen_entity), "bval")]),
         (inputnode, ds_report_stdev, [("name_source", "source_file"),
                                       (("in_shells", _gen_entity), "bval")]),
+        (inputnode, ds_report_noise, [("name_source", "source_file"),
+                                      (("in_shells", _gen_entity), "bval")]),
         (mosaic_mean, ds_report_mean, [("out_file", "in_file")]),
         (mosaic_stddev, ds_report_stdev, [("out_file", "in_file")]),
+        (mosaic_noise, ds_report_noise, [("out_file", "in_file")]),
     ])
     # fmt: on