diff --git a/docs/methods.rst b/docs/methods.rst index a149806c8a..04cf2b491d 100644 --- a/docs/methods.rst +++ b/docs/methods.rst @@ -56,18 +56,29 @@ we obtain the nonzero component of the associated displacements field Direct B0 mapping sequences ~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.. admonition:: BIDS Specification + + See `this section of the BIDS specification + `__. + Some MR schemes such as :abbr:`SEI (spiral-echo imaging)` can directly reconstruct an estimate of *the fieldmap in Hz*, :math:`V(i,j,k)`. These *fieldmaps* are described with more detail `here `__. -This corresponds to `this section of the BIDS specification -`__. - .. _sdc_phasediff : Phase-difference B0 estimation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.. admonition:: BIDS Specification + + See `this section of the BIDS specification + `__. + + Some scanners produce one ``phasediff`` map, where the drift between the two echos has + already been calculated, see `the corresponding section of BIDS + `__. + The fieldmap variation in T, :math:`\Delta B_0 (i, j, k)`, that is necessary to obtain :math:`\Delta_\text{PE} (i, j, k)` in Eq. :math:`\eqref{eq:fieldmap-1}` can be calculated from two subsequient :abbr:`GRE (Gradient-Recalled Echo)` echoes, @@ -97,23 +108,20 @@ the range :math:`[0 \dotsb 2\pi )`. It is necessary to find the integer number of offsets that make a region continuously smooth with its neighbors (*phase-unwrapping*, [Jenkinson2003]_). -This corresponds to `this section of the BIDS specification -`__. -Some scanners produce one ``phasediff`` map, where the drift between the two echos has -already been calculated (see `the corresponding section of BIDS -`__). - .. _sdc_pepolar : :abbr:`PEPOLAR (Phase Encoding POLARity)` techniques ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.. admonition:: BIDS Specification + + See `this section of the BIDS specification + `__. + Alternatively, it is possible to estimate the field by exploiting the symmetry of the distortion when the PE polarity is reversed. *SDCFlows* integrates two implementations based on FSL ``topup`` [Andersson2003]_, and AFNI ``3dQwarp`` [Cox1997]_. - -This corresponds to `this section of the BIDS specification -`__. +By default, FSL ``topup`` will be used. .. _sdc_fieldmapless :