RPT: Improve and align captions with now-produced reportlets [no fasttrack]

Author: effigies

fmriprep/data/reports-spec.yml

@@ -82,7 +82,7 @@ sections:
       Overlaid on top of the co-registration results, the final BOLD mask is represented
       with a red contour for reference.
     static: false
-    subtitle: Alignment between the anatomical reference of the fieldmap and the target EPI (debug mode)
+    subtitle: Alignment between the anatomical reference of the fieldmap and the target EPI
   - bids: {datatype: figures, desc: fieldmap, suffix: bold}
     caption: Estimated fieldmap, as reconstructed on the target BOLD run space to allow
       the assessment of its alignment with the distorted data.
@@ -97,7 +97,9 @@ sections:
     subtitle: "Reconstructed <em>B<sub>0</sub></em> map in the corresponding run's space (debug mode)"
   - bids: {datatype: figures, desc: sdc, suffix: bold}
     caption: Results of performing susceptibility distortion correction (SDC) on the
-      EPI
+      BOLD reference image. The "distorted" image is the image that would be used to
+      align to the anatomical reference if SDC were not applied. The "corrected"
+      image is the image that was used.
     static: false
     subtitle: Susceptibility distortion correction
   - bids: {datatype: figures, desc: forcedsyn, suffix: bold}
@@ -118,37 +120,15 @@ sections:
       appear in the 100ms bin.
     static: false
     subtitle: T2* gray-matter values
-  - bids: {datatype: figures, desc: flirtnobbr, suffix: bold}
-    caption: <code>mri_coreg</code> (FreeSurfer) was used to generate transformations
-      from EPI space to T1 Space - BBR refinement using FSL <code>flirt</code> rejected.
-      Note that Nearest Neighbor interpolation is used in the reportlets in order to
-      highlight potential spin-history and other artifacts, whereas final images are
-      resampled using Lanczos interpolation.
-    static: false
-    subtitle: Alignment of functional and anatomical MRI data (volume based)
   - bids: {datatype: figures, desc: coreg, suffix: bold}
-    caption: <code>mri_coreg</code> (FreeSurfer) was used to generate transformations
-      from EPI space to T1 Space - <code>bbregister</code> refinement rejected. Note
-      that Nearest Neighbor interpolation is used in the reportlets in order to highlight
-      potential spin-history and other artifacts, whereas final images are resampled
-      using Lanczos interpolation.
-    static: false
-    subtitle: Alignment of functional and anatomical MRI data (volume based)
-  - bids: {datatype: figures, desc: flirtbbr, suffix: bold}
-    caption: FSL <code>flirt</code> was used to generate transformations from EPI-space
-      to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain
-      tissue segmentation) was used for BBR. Note that Nearest Neighbor interpolation
-      is used in the reportlets in order to highlight potential spin-history and other
-      artifacts, whereas final images are resampled using Lanczos interpolation.
-    static: false
-    subtitle: Alignment of functional and anatomical MRI data (surface driven)
-  - bids: {datatype: figures, desc: bbregister, suffix: bold}
-    caption: <code>bbregister</code> was used to generate transformations from EPI-space
-      to T1w-space. Note that Nearest Neighbor interpolation is used in the reportlets
-      in order to highlight potential spin-history and other artifacts, whereas final
-      images are resampled using Lanczos interpolation.
+    caption: This panel shows the alignment of the reference EPI (BOLD) image to the
+      anatomical (T1-weighted) image.
+      The reference EPI has been contrast enhanced and susceptibility-distortion
+      corrected (if applicable) for improved anatomical fidelity.
+      The anatomical image has been resampled into EPI space, as well as the
+      anatomical white matter mask, which appears as a red contour.
     static: false
-    subtitle: Alignment of functional and anatomical MRI data (surface driven)
+    subtitle: Alignment of functional and anatomical MRI data (coregistration)
   - bids: {datatype: figures, desc: rois, suffix: bold}
     caption: Brain mask calculated on the BOLD signal (red contour), along with the
       regions of interest (ROIs) used for the estimation of physiological and movement

fmriprep/workflows/bold/fit.py

@@ -354,6 +354,7 @@ def init_bold_fit_wf(
         ]),
         (outputnode, func_fit_reports_wf, [
             ("coreg_boldref", "inputnode.coreg_boldref"),
+            ("bold_mask", "inputnode.bold_mask"),
             ("boldref2anat_xfm", "inputnode.boldref2anat_xfm"),
         ]),
         (summary, func_fit_reports_wf, [("out_report", "inputnode.summary_report")]),

fmriprep/workflows/bold/outputs.py

@@ -195,6 +195,7 @@ def init_func_fit_reports_wf(
         "source_file",
         "sdc_boldref",
         "coreg_boldref",
+        "bold_mask",
         "boldref2anat_xfm",
         "boldref2fmap_xfm",
         "t1w_preproc",
@@ -368,7 +369,8 @@ def init_func_fit_reports_wf(
             ]),
             (inputnode, sdcreg_report, [
                 ('sdc_boldref', 'reference'),
-                ('fieldmap', 'fieldmap')
+                ('fieldmap', 'fieldmap'),
+                ('bold_mask', 'mask'),
             ]),
             (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]),
             (inputnode, ds_sdcreg_report, [('source_file', 'source_file')]),