enh: update visual report specification with fieldmaps
@@ -26,12 +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: Fieldmaps
- ordering: session
+
+- name: <em>B<sub>0</sub></em> field mapping
+ ordering: session,acquisition,run,fmapid
reportlets:
- - bids: {datatype: figures, desc: brain, suffix: fieldmap}
- caption: Brain extraction of the magnitude image from the fieldmap.
- subtitle: Skull stripped magnitude image
+ - 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:
