Elongated Brain: Errors in fMRIprep Susceptibility Distortion Correction

Summary of what happened:

Hello Neurostars, I am having trouble with SDC in fmriprep using field maps, please help!

I am using fmriprep to preprocess resting state and task based fmri scans, with a fieldmap, using the CMRR mb sequence. the images are getting considerably more distorted following SDC in fmriprep. I believe I am having a similar issue to this thread, but the posters did not seem to reach a conclusion.

I am using fmriprep version 23.1.04 on a high performance computing cluster, using singularity (fmriprep_23.1.04-001.sif) and slurm (the batch submission system).

I converted the raw dicoms to nifti and put them into bids format with heudiconv. I then checked the bids compliance with the bids validator, and only received minor warnings (readme file was small).

I tried using the flag --use-syn-sdc, but got the same result.

Here are images from the fmriprep html output.


and the fieldmaps:

Command used (and if a helper script was used, a link to the helper script or the command generated):

This is the code I used to run the fmriprep.sif image:

singularity run -B ${SINGULARITYENV_TEMPLATEFLOW_HOME:-$SCRATCH/software/templateflow}:/templateflow --cleanenv --home $SCRATCH -B $SCRATCH:/work $SCRATCH/software/fmriprep_23.1.4.sif ${bidsdir} ../fmriprep participant --participant-label ${subject} --fs-license-file $FS_LICENSE --me-output-echos --me-t2s-fit-method curvefit --nthreads 16 --omp-nthreads 16


The software I am using (all as singularity images)
fmriprep version 23.1.04
heudiconv version 1.0.1
bidsva.idator version 1.14.0

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity on an HPC that uses Debian as the OS and Slurm for batch submission

Data formatted according to a validatable standard? Please provide the output of the validator:

Here are my bids validator warnings (most seem benign to me):


(node:122560) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
	e[33m1: [WARN] Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing. (code: 38 - INCONSISTENT_SUBJECTS)e[39m

	e[33m2: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)e[39m

e[33m3: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)e[39m

Screenshots / relevant information:

Any inclination as to what might be happening? Any and all help is very much appreciated. I hope I have been adequately detailed in this post about my issue. However, I am happy to provide any further information as needed.


Hi @jackpmanning and welcome to neurostars!

Does this error persist with the most recent stable release, 23.2.0? Is this error consistent across subjects? What kind of fmaps are these? Have you confirmed the phase encoding directions of your BOLD/fmap images?


Howdy Steven,

Thank you for the suggestion, that seems to have fixed the issue!

1 Like