Plot CIFTI maps on subject-specific surfaces when available (PennLINC…

…#1208)
tsalo · Jul 23, 2024 · 9af82a7 · 9af82a7
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diff --git a/docs/outputs.rst b/docs/outputs.rst
@@ -125,6 +125,10 @@ Surface mesh files
 If the ``--warp-surfaces-native2std`` option is selected, and reconstructed surfaces are available
 in the preprocessed dataset, then these surfaces will be warped to fsLR space at 32k density.
 
+The resulting mesh files will reflect the subject's morphology with the same geometry and density
+as fsLR-32k surfaces, which may be useful for visualizing fsLR-space derivatives on a subject's
+brain.
+
 .. code-block::
 
    xcp_d/

diff --git a/xcp_d/data/reports-spec-func.yml b/xcp_d/data/reports-spec-func.yml
@@ -30,7 +30,22 @@ sections:
       datatype: figures
       desc: coverage
       suffix: bold
-    caption:  Parcellation coverage.
+    caption: |
+      Parcellation coverage.
+    subtitle: Coverage
+  - bids:
+      datatype: figures
+      desc: coverageParcellatedStandard
+      suffix: bold
+    caption: |
+      Parcellation coverage, overlaid on the fsLR template surface.
+    subtitle: Coverage
+  - bids:
+      datatype: figures
+      desc: coverageParcellatedSubject
+      suffix: bold
+    caption: |
+      Parcellation coverage, overlaid on the subject's surface warped to the fsLR template.
     subtitle: Coverage
   - bids: {datatype: figures, desc: connectivityplot, suffix: bold}
     caption:  This plot shows heatmaps from ROI-to-ROI correlations from one to four atlases.
@@ -44,16 +59,40 @@ sections:
     subtitle: ALFF
   - bids:
       datatype: figures
-      desc: alffSurfacePlot
+      desc: alffSurfaceStandard
       suffix: bold
-    caption:  ALFF, or amplitude of low frequency fluctuations.
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations, overlaid on the fsLR template surface.
+    subtitle: ALFF
+  - bids:
+      datatype: figures
+      desc: alffSurfaceSubject
+      suffix: bold
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations, overlaid on the subject's surface
+      warped to the fsLR template.
     subtitle: ALFF
   - bids:
       datatype: figures
       desc: alffParcellated
       suffix: bold
     caption:  Parcellated ALFF.
     subtitle: ALFF
+  - bids:
+      datatype: figures
+      desc: alffParcellatedStandard
+      suffix: bold
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations, overlaid on the fsLR template surface.
+    subtitle: ALFF
+  - bids:
+      datatype: figures
+      desc: alffParcellatedSubject
+      suffix: bold
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations, overlaid on the subject's surface
+      warped to the fsLR template.
+    subtitle: ALFF
   - bids:
       datatype: figures
       desc: rehoVolumetricPlot
@@ -63,16 +102,41 @@ sections:
     subtitle: ReHo
   - bids:
       datatype: figures
-      desc: rehoSurfacePlot
+      desc: rehoSurfaceStandard
       suffix: bold
-    caption:  ReHo, or regional homogeneity.
+    caption: |
+      ReHo, or regional homogeneity.
+      Overlaid on the fsLR midthickness surface.
+    subtitle: ReHo
+  - bids:
+      datatype: figures
+      desc: rehoSurfaceSubject
+      suffix: bold
+    caption: |
+      ReHo, or regional homogeneity.
+      Overlaid on the participant's midthickness surface mapped onto fsLR space.
     subtitle: ReHo
   - bids:
       datatype: figures
       desc: rehoParcellated
       suffix: bold
     caption:  Parcellated ReHo.
     subtitle: ReHo
+  - bids:
+      datatype: figures
+      desc: rehoParcellatedStandard
+      suffix: bold
+    caption: |
+      ReHo, or regional homogeneity, overlaid on the fsLR template surface.
+    subtitle: ReHo
+  - bids:
+      datatype: figures
+      desc: rehoParcellatedSubject
+      suffix: bold
+    caption: |
+      ReHo, or regional homogeneity, overlaid on the subject's surface
+      warped to the fsLR template.
+    subtitle: ReHo
 - name: About
   reportlets:
   - bids: {datatype: figures, desc: about, suffix: bold}
diff --git a/xcp_d/data/reports-spec.yml b/xcp_d/data/reports-spec.yml
@@ -40,6 +40,20 @@ sections:
       suffix: bold
     caption:  Parcellation coverage.
     subtitle: Coverage
+  - bids:
+      datatype: figures
+      desc: coverageParcellatedStandard
+      suffix: bold
+    caption: |
+      Parcellation coverage, overlaid on the fsLR template surface.
+    subtitle: Coverage
+  - bids:
+      datatype: figures
+      desc: coverageParcellatedSubject
+      suffix: bold
+    caption: |
+      Parcellation coverage, overlaid on the subject's surface warped to the fsLR template.
+    subtitle: Coverage
   - bids: {datatype: figures, desc: connectivityplot, suffix: bold}
     caption:  This plot shows heatmaps from ROI-to-ROI correlations from one to four atlases.
     subtitle: Correlation Heatmaps from A Subset of Atlases
@@ -48,20 +62,45 @@ sections:
       desc: alffVolumetricPlot
       suffix: bold
     caption:  ALFF, or amplitude of low frequency fluctuations.
-              Overlaid on T1W image with same entities as the original image.
+              Overlaid on T1w image with same entities as the original image.
     subtitle: ALFF
   - bids:
       datatype: figures
-      desc: alffSurfacePlot
+      desc: alffSurfaceStandard
       suffix: bold
-    caption:  ALFF, or amplitude of low frequency fluctuations.
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations.
+      Overlaid on the fsLR midthickness surface.
+    subtitle: ALFF
+  - bids:
+      datatype: figures
+      desc: alffSurfaceSubject
+      suffix: bold
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations.
+      Overlaid on the participant's midthickness surface mapped onto fsLR space.
     subtitle: ALFF
   - bids:
       datatype: figures
       desc: alffParcellated
       suffix: bold
     caption:  Parcellated ALFF.
     subtitle: ALFF
+  - bids:
+      datatype: figures
+      desc: alffParcellatedStandard
+      suffix: bold
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations, overlaid on the fsLR template surface.
+    subtitle: ALFF
+  - bids:
+      datatype: figures
+      desc: alffParcellatedSubject
+      suffix: bold
+    caption: |
+      ALFF, or amplitude of low frequency fluctuations, overlaid on the subject's surface
+      warped to the fsLR template.
+    subtitle: ALFF
   - bids:
       datatype: figures
       desc: rehoVolumetricPlot
@@ -71,16 +110,41 @@ sections:
     subtitle: ReHo
   - bids:
       datatype: figures
-      desc: rehoSurfacePlot
+      desc: rehoSurfaceStandard
       suffix: bold
-    caption:  ReHo, or regional homogeneity.
+    caption: |
+      ReHo, or regional homogeneity.
+      Overlaid on the fsLR midthickness surface.
+    subtitle: ReHo
+  - bids:
+      datatype: figures
+      desc: rehoSurfaceSubject
+      suffix: bold
+    caption: |
+      ReHo, or regional homogeneity.
+      Overlaid on the participant's midthickness surface mapped onto fsLR space.
     subtitle: ReHo
   - bids:
       datatype: figures
       desc: rehoParcellated
       suffix: bold
     caption:  Parcellated ReHo.
     subtitle: ReHo
+  - bids:
+      datatype: figures
+      desc: rehoParcellatedStandard
+      suffix: bold
+    caption: |
+      ReHo, or regional homogeneity, overlaid on the fsLR template surface.
+    subtitle: ReHo
+  - bids:
+      datatype: figures
+      desc: rehoParcellatedSubject
+      suffix: bold
+    caption: |
+      ReHo, or regional homogeneity, overlaid on the subject's surface
+      warped to the fsLR template.
+    subtitle: ReHo
 - name: About
   reportlets:
   - bids: {datatype: figures, desc: about, suffix: bold}