[fMRIPrep] No susceptibility distortion correction despite "IntendedFor" field in fmap .json files

[Steven]

Hi @samlyons,

Perhaps you will have better luck using the B0FieldIdentifier/B0FieldSource method? See here: FmriPrep SDC Fails to Associate To Bold Image, Preprocess Working - #10 by emdupre

But before that, lets also fix some things about your command:

@samlyons

    /project/gottfried/samlyons/images/fmriprep-23.0.2.simg \
    /project/gottfried/samlyons/olfunc/sub-olfunc007/ses-olfunc007 \
    /project/gottfried/samlyons/olfunc/derivatives \

It looks like you are inputting a subject folder to fMRIPrep. You should be putting in the root directory.

@samlyons

    --fs-no-reconall

This flag is not recommended (see here).

@samlyons

-B /project/gottfried/samlyons/olfunc:/data \
    -B /project/gottfried/samlyons/olfunc/derivatives:/olfunc/derivatives \
    -B /project/gottfried/samlyons/work:/work \
    -B /project/gottfried/samlyons/images/license.txt:/license.txt \
    -B /project/gottfried/samlyons/olfunc \

You make these bindings, but do not use some of them (in particular /data and /olfunc/derivatives).

Try this as your command (I am also removing the skip-bids-validation in case something BIDS related is causing a problem):

unset PYTHONPATH; singularity run --cleanenv -B /project/gottfried/samlyons/olfunc:/data \
    -B /project/gottfried/samlyons/olfunc/derivatives:/derivatives \
    -B /project/gottfried/samlyons/work:/work \
    -B /project/gottfried/samlyons/images/license.txt:/license.txt \
    /project/gottfried/samlyons/images/fmriprep-23.0.2.simg \
    /data \
    /derivatives \
    participant \
    --participant-label olfunc007 \
    --fs-license-file /license.txt \
    --stop-on-first-crash \
    --nthreads 16 \
    --omp-nthreads 16 \
    -w /work \

Best,
Steven