fmriprep: Avoiding sbrefs for the coregistration reference causes poor registration in low contrast multiband sequences

What happened?

Reported in https://neurostars.org/t/poor-func-anatomical-registration-with-fmriprep-21-0-2-on-multi-echo-data-set/26217, coregistration is poor. We currently use sbrefs for the initial boldref, but not for the final, which means that we have the benefit of high contrast for HMC, where it matters less, and not for coregistration, where it matters more.

What command did you use?

singularity run --cleanenv -B /projects/:/projects/\
    -B ${WORK_DIR}:/quest_scratch \
    /projects/singularity_images/fmriprep-21.0.2.simg \
    ${BIDS_DIR} \
    ${BIDS_DIR}/${DERIVS_DIR} \
    participant --participant-label ${subject} \
    -w /quest_scratch --omp-nthreads 8 --nthreads 16 \
    --fs-license-file /projects/singularity_images/freesurfer_license.txt \
    --fs-subjects-dir ${BIDS_DIR}/${DERIVS_DIR}/sourcedata/freesurfer \
    --output-spaces MNI152NLin6Asym:res-2 \
    --ignore slicetiming --fd-spike-threshold 0.2 --me-output-echos --resource-monitor

What version of fMRIPrep are you running?

21.0.2 and 23.0.2

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

About this issue

Original URL
State: closed
Created a year ago
Comments: 20 (12 by maintainers)

Most upvoted comments

This won’t work:

  "sbref": {"datatype": "func", "suffix": "part-mag_sbref"},

You’ll need to specify the part entity:

  "sbref": {"datatype": "func", "suffix": "sbref", "part": [null, "mag"]},

That will accept files that either do not have a part entity, or part == "mag".

Also, you only need to update the filters that you’re changing from the default, so your whole file could be:

{
  "sbref": {"datatype": "func", "suffix": "sbref", "part": [null, "mag"]}
}

effigies on Aug 21, 2023