Merge pull request #56 from nipreps/fix/sdcflows-integration

ENH: Add estimated field maps to final reports

Author: oesteban

nibabies/data/reports-spec.yml

@@ -26,6 +26,51 @@ sections:
     caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>)
       overlaid on the participant's T1w template.
     subtitle: Surface reconstruction
+
+- name: <em>B<sub>0</sub></em> field mapping
+  ordering: session,acquisition,run,fmapid
+  reportlets:
+  - bids: {datatype: figures, desc: mapped, suffix: fieldmap}
+    caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
+      along the phase-encoding direction of the image. Some scanners produce a <em>B<sub>0</sub></em>
+      mapping of the field, using Spiral Echo Imaging (SEI) or postprocessing a "phase-difference"
+      acquisition. The plot below shows an anatomical "magnitude" reference and the corresponding
+      fieldmap.
+    description: Hover over the panels with the mouse pointer to also visualize the intensity of the
+      field inhomogeneity in Hertz.
+    static: false
+    subtitle: "Preprocessed <em>B<sub>0</sub></em> mapping acquisition"
+  - bids: {datatype: figures, desc: phasediff, suffix: fieldmap}
+    caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
+      along the phase-encoding direction of the image. A Gradient-Recalled Echo (GRE) scheme for the
+      mapping of the <em>B<sub>0</sub></em> inhomogeneities by subtracting the phase maps obtained at
+      two subsequent echoes. The plot below shows an anatomical "magnitude" reference and the corresponding
+      fieldmap.
+    description: Hover over the panels with the mouse pointer to also visualize the intensity of the
+      field inhomogeneity in Hertz.
+    static: false
+    subtitle: "Preprocessed mapping of phase-difference acquisition"
+  - bids: {datatype: figures, desc: pepolar, suffix: fieldmap}
+    caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
+      along the phase-encoding direction of the image. Utilizing two or more images with different
+      phase-encoding polarities (PEPolar) or directions, it is possible to estimate the inhomogeneity
+      of the field. The plot below shows a reference EPI (echo-planar imaging) volume generated
+      using two or more EPI images with varying phase-encoding blips.
+    description: Hover on the panels with the mouse pointer to also visualize the intensity of the
+      inhomogeneity of the field in Hertz.
+    static: false
+    subtitle: "Preprocessed estimation with varying Phase-Endocing (PE) blips"
+  - bids: {datatype: figures, desc: anat, suffix: fieldmap}
+    caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions
+      along the phase-encoding direction of the image. Utilizing an <em>anatomically-correct</em> acquisition
+      (for instance, T1w or T2w), it is possible to estimate the inhomogeneity of the field by means of nonlinear
+      registration. The plot below shows a reference EPI (echo-planar imaging) volume generated
+      using two or more EPI images with the same PE encoding, after alignment to the anatomical scan.
+    description: Hover on the panels with the mouse pointer to also visualize the intensity of the
+      inhomogeneity of the field in Hertz.
+    static: false
+    subtitle: "Preprocessed estimation by nonlinear registration to an anatomical scan (&ldquo;<em>fieldmap-less</em>&rdquo;)"
+
 - name: Functional
   ordering: session,task,acquisition,ceagent,reconstruction,direction,run,echo
   reportlets: