Summary of what happened:
Hi everyone,
I’ve noticed an image artifact in the raw data of one of my participants, present in the structural, functional, and spin-echo images. I’m concerned about its potential impact on my analysis. My functional dataset consists of a slab of 27 slices positioned over S1. You can find the raw images below.
I processed the data using fMRIPrep with the same pipeline as for the other participants. While coregistration looks reasonable in participant space (please correct me if I’m wrong), I have some concerns about the alignment in MNI space (it looks like it’s pulled up because of the artifact).
Would you recommend excluding this participant? Could improving segmentation help? Any insights or suggestions would be greatly appreciated! (I already tried with the new fmriprep version, and the coregister is worst)
Thanks in advance!
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run -ti --rm \
-v /DATAPOOL/SOMATOMAP/BIDS2025:/data:ro \
-v /DATAPOOL/SOMATOMAP/BIDS2025/derivatives/fmriprep_boldheader_2025:/out \
-v /SCRATCH/users/user1/fmriprep-work_S1Map_boldheader_2025:/work \
-v /DATAPOOL/SOMATOMAP/BIDS2025/freesurfer/license.txt:/license \
nipreps/fmriprep:23.1.3 \
/data /out/fmriprep \
participant \
-w /work \
--fs-license-file /license \
--bold2t1w-init header \
--nprocs 18 \
--skip_bids_validation \
--stop-on-first-crash \
--output-spaces T1w func MNI152NLin2009cAsym \
--participant-label p0001
Version:
23.1.3
Environment (Docker, Singularity / Apptainer, custom installation):
docker
Data formatted according to a validatable standard? Please provide the output of the validator:
yes
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
Screenshots / relevant information:
Raw images
Structural (I cut to only show the area that is causing the artifact - highlighted in red)
Functional (slab with 27 slices):
Spin echoes:
Preprocessed structural images
Participant space:
MNI space:
Preprocessed functional images
Participant space (desc-preproc_bold in orange with some transparency):
MNI space (desc-preproc_bold in orange with some transparency):
