Fmriprep aliasing in fieldmap plus error

1

Hi all,

Thanks for great work on building the fmriprep pipeline. A great initiative that I look forward to using more in the future. Hopefully somebody can help me fix some fieldmap issues!

I am using a multiband (3) multi echo (3) sequence on a siemens 3T scanner and I also collected fieldmaps (phasediff + 2 maginute images). I transformed my data to bids structure and tested it on the bids validator. However, it seems that something is going wrong. There seems to be aliasing in my magnitude images. How does fmriprep handle this problem? Do you know how this affects my output data? Would it be better for now, for this subject to not apply the fieldmaps but use use the flag --use-syn-sdc only?

Here the output html file, for this output I used both fieldmaps and --use-yn-sdc. There are also errors created that I do not understand:

https://drive.google.com/file/d/1QhQv270VGhGUvj_GzWuoqS3dl4B42UbC/view?usp=sharing

Any help is welcome is more information is required please let me know,

Thanks,
Inge

EDIT
Apparently google & dropbox don’t support html anymore, link is a pdf.

2

Indeed the Field of View set for the fieldmap is really bad

image
image.jpg1865×896 485 KB

I would recommend not using fieldmap correction for this particiapatn (--ignore fieldmaps) and using fielmapless correction (--use-syn-scd).

3

Hi Chris,

Thanks for your help! I will use your suggested strategy.

Best
Inge