fMRIPrep Preprocessing issues

Software Support
1

Summary of what happened:

Hi all,

I have some artifacts generated after preprocessing in fmriprep. It seems like there is something going wrong in the preprocessing that pulls/stretches the brain down from the brainstem and up from the motor cortex above it. Please see the image of preprocessed data.

In the html reports, everything seems normal though.

Currently only the default paramteres are used (fMRIPrep version: 25.1.3) and this seems to be prevalent among the whole data set. Any idea as to whty this is happening?

I am analysing fmri data for the first time and any help is much appreciated!

Thanks a lot in advance,
Ann

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

    fmriprep-docker $bids_root_dir $bids_root_dir/derivatives \
        participant \
        --participant-label $subj \
        --md-only-boilerplate \
        --ignore fieldmaps \
        --fs-license-file $FS_LICENSE\
        --fs-no-reconall \
        --output-spaces MNI152NLin2009cAsym:res-2 \
        --nthreads $nthreads \
        --stop-on-first-crash \
        --mem_mb $mem_mb \
        --skip-bids-validation

Version:

25.1.3

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

DOCKER with fmriprep-docker

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

not yet checked

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

sub-10_run-03_processed
sub-10_run-03_processed730×350 24.2 KB

2

Hi @AXC and welcome to neurostars!

In the future please use the Software Support post category and prepopulated template for these kind of questions. You can see I edited your post for you this time. You can edit your post to add the missing information.

How does the brain mask look - does it include these artifacts? What do the raw data look like? Is that artifact in all the volumes? Was any susceptibility distortion correction performed (i.e., with fieldmaps)?

Best,
Steven

1 Like
3

This is probably Interpolation effect when the brain signal goes right up to the edge of the image · Issue #3475 · nipreps/fmriprep · GitHub and will be fixed in the pending release. You can test with nipreps/fmriprep:unstable.

2 Likes
4

Thank you all very much! I now ran it with

    docker run --rm -e DOCKER_VERSION_8395080871=28.3.3 -it -v /srv/shareMRI/fmriprep_preprocessing/BIDS/license.txt:/opt/freesurfer/license.txt:ro -v /srv/shareMRI/fmriProcess2/BIDS:/data:ro -v /srv/shareMRI/fmriProcess2/BIDS/derivatives:/out nipreps/fmriprep:unstable /data /out participant --participant-label $subj  --md-only-boilerplate --ignore fieldmaps --fs-no-reconall --nthreads 4 --stop-on-first-crash --mem_mb 15000 --skip-bids-validation --output-spaces MNI152NLin2009cAsym:res-2

and the issue seems to have been fixed!