PhaseEncodingDirection

1

Hello,
I was under the impression that we actually use epi_AP( A>P which is “j-“ ) (field maps) to perform distortion correction of BOLD_AP ( A>P , also "j-“). However, fmripep-pipeline ( https://fmriprep.readthedocs.io/en/0.4.4/sdc/unwarping.html) need opposing direction for this purpose.

If so, in epi.JSON file of fieldmap_AP, at "IntendedFor” I should point the BOLD_image_PA (P>A, bold data collected with opposing phaseEncodingDirection)? please correct me if i am wrong.

Could you please help me understanding this ?

Thanks
BL

2

This is correct.

In other words you need to have data from at least two different phase encoding directions (for example two opposite directions) to be able to estimate field susceptibility and correct distortions. You can find more information at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup and https://doi.org/10.1016/S1053-8119(03)00336-7

3

Thank you Chris,
I am running fmriprep-docker ( and still running …)–but keep throwing following warning message at terminal but any suggestion on this, why and how to resolve this ?

Running “rois_plot” (“niworkflows.interfaces.masks.ROIsPlot”)
warnings.warn(“No contour levels were found”
/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range…