Fmriprep Susceptibility distortion correction: None

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#1

Hi,

I am using fmriprep v20.2.1 via the fmriprep-docker container and I have fieldmaps available for my dataset (in the /fmap/ folder). The BIDS validator does not give me any error/ warning, however the fmriprep output summary says:

Susceptibility distortion correction: None

As I understand no specific argument is necessary in order to invoke distortion correction. The pipeline runs without error.

I read somewhere else about an “IntendedFor” field in the fieldmap’s .json files - is this required now and wasn’t previously?

I had used an older version of fmriprep (v1.5.2) previously on another dataset and fieldmap correction were automatically conducted.

Thanks in advance.

Marius

#2

Yes, in the bids fmap folder, you should put an intended for field in the JSON files so fmriprep can associate them (or use the fieldmapless distortion method, syn-sdc). I have a simple script to automate this in jupyter / python, let me know if you’d want it.

Best,
Steven

1 Like
#3

Thanks, Steven. I would appreciate if you send me the script. I also found it now in the bids-specification docs.
Best, Marius

#4

Hi Steven,
I’m running into this same problem now - if you don’t mind also sharing your script with me, it’d be much appreciated!

Thanks,
Fareshte