Add recommendations for distortion correction (#896)

* Add a FAQ.

* Add a subsection to the processing section on SDC.

* Update faq.rst

* Remove mentions of ultra-high resolution data.

* Apply suggestions from code review

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

---------

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

docs/faq.rst

@@ -193,3 +193,22 @@ Yes, these techniques are complementary.
 Multiband fMRI leads to collecting multiple slices within a volume  simultaneously, while multi-echo
 fMRI is instead related to collecting multiple unique volumes.
 These techniques can be combined to reduce the TR in a multi-echo sequence.
+
+********************************************************************************
+[ME-fMRI] How do field maps and distortion correction work with multi-echo fMRI?
+********************************************************************************
+
+There are many different approaches to susceptibility distortion correction out there- far too many to discuss here.
+However, the good news is that distortion does not typically change across echoes in multi-echo fMRI.
+In most cases, the readout acquisition type and total readout time are the same for each echo,
+so distortion will remain relatively constant, even as dropout increases with echo time.
+
+What this means is that, in the vast majority of multi-echo datasets,
+standard distortion correction methods will work, and should be applied in the same manner on all echoes.
+For example, if you acquire a blip-up/blip-down set of images for all of your echo times,
+you should use the first echo time's images to generate the undistortion transform,
+as long as that first echo has sufficient gray/white constrast to be useful for alignment
+(in which case, use the earliest echo that does have good contrast).
+
+For context, please see
+`this NeuroStars thread <https://neurostars.org/t/multi-echo-pepolar-fieldmaps-bids-spec-sdcflows-grayzone/23933/5>`_.

docs/multi-echo.rst

@@ -462,6 +462,19 @@ time point.
     research to better understand how these steps can be applied before denoising.
 
 
+4. Apply susceptibility distortion correction consistently across echoes
+========================================================================
+
+One key feature of susceptibility distortion is that it is primarily a factor of readout pattern and total readout time, rather than echo time.
+This means that, for most multi-echo sequences, even though dropout will increase with echo time,
+distortion will not (at least not to a noticeable/meaningful extent).
+
+For this reason, if you are applying TOPUP-style (blip-up/blip-down) "field maps",
+we recommend using your first echo time, as this will exhibit the least dropout.
+If your first echo time is very short, and exhibits poor gray/white contrast, then a later echo time may be preferable.
+In any case, you should calculate the spatial transform from just one of your echoes and apply it across all of them.
+
+
 .. _fMRIPrep: https://fmriprep.readthedocs.io
 .. _afni_proc.py: https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html