Fmriprep Susceptibility distortion correction: None

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

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

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

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