Increased distortions following distortion correction in FMRIPREP?

[jsein]

Hi @jimmywyngaarden ,

What kind of SDC method do you use for your data?

There has been numerous reports of difficulties of SDC with fmriprep for case 1, 2 and 3.

See for example here:

Fieldmap correction gone wrong

Summary of what happened: I am running fmriprep on my data with fieldmap (2 magnitude images + 1 phase diff image). The output image looks weird, and very distorted. Any idea on possible reason? Command used (and if a helper script was used, a link to the helper script or the command generated): export SINGULARITYENV_TEMPLATEFLOW_HOME=/home/fmriprep/.cache/templateflow /usr/bin/singularity run \ --contain \ --cleanenv \ -B /tmp -B /data -B /data1 -B /data2 -B /data3 -B /n -B /cm…

and here:

Different sdc results for fmriprep versions 21.0.2 and 23.0.2

I got what I believe are reasonable results from susceptibility distortion correction with fMRIprep version 21.0.2. Here is a snapshot of the fieldmap from the output report with v21.0.2: [fieldmap_v21.0.2] And here is a snapshot of the sdc results from the report with v21.0.2: [sdc_bold_v21.0.2] I got different/unusual results when using v23.0.2 to process the same data. Here is a snapshot of the fieldmap from the output report for v23.0.2: [fieldmap_v23.0.2] And here are the sdc resul…