[FMRIprep] "SDC was omitted"

1

Hi all,

I am using fmrirprep 1.5.8 and I have a BIDS-valid /fmap (blip-up/blip-down) directory under my BIDS data directory. However, in my CITATION.md, it states that ‘Susceptibility Distortion Correction (SDC) was omitted’. May I what could possibly cause this and how I should include SDC as a preprocessing step?

Thanks!

2

do you have fieldmap?
and can you post your command line?

4

The command line is as following:
singularity run -B ${root_dir}:${root_dir} --home ${root_dir} --cleanenv ${base_dir}/fmriprep-1.5.8.simg $BIDS_data_dir $output_dir participant --participant-label $subject_id --work-dir $working_dir --fs-license-file $fs_license --omp-nthreads 16 --nthreads 16 -t $task

I am using singularity 3.5.2 to run fmriprep, and I have changed my root directory to another directory (i.e. ${root_dir}), instead of $HOME . $BIDS_data_dir is my BIDS-validated directory, I have two opposite phase encoding (AP and PA) fieldmaps.

Thanks!

5

This is because of a missing “IntendedFor” field in the fmap json file.