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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Weird fieldmap image induce misalignment in v24.0.0 #3389

Open Blink621 opened 4 weeks ago

Blink621 commented 4 weeks ago

What happened?

Hi, I'm using the fmriprep 24.0.0 to preprocess my data. I found in some runs, the output of fieldmap image are weird, whose intensity of the field inhomogeneity are distributed across the brain. This fieldmap would induce large movement of the distortion correction process. However, in other fieldmap data, the intensity are aggregated in the cavity at the base of the brain. The distortion correction based on these fieldmap are much more stable. I'm wondering why the weird fieldmap image are generated. Is this related with the quality of our data, or some steps I was missed when using fmriprep? Also, how does the intensity distribution of the field inhomogeneity imply, is the high value in the cavity normal?

Weird fieldmap image: intensity of the field inhomogeneity are distributed across the brain image

Weird fieldmap image induce large movement of the distortion correction image

Other fieldmap data: the intensity are aggregated in the cavity at the base of the brain image

What command did you use?

docker run -ti --rm \
-v $niftidir:/data:ro \
-v $outdir/wkdir:/work \
-v $outdir/fmriprep:/out \
-v $licensedir:/licensedir \
-u $(id -u):$(id -g) \
nipreps/fmriprep:24.0.0 /data /out participant -w /work \
--skip-bids-validation --participant-label 03 --nprocs 64 \
--output-spaces anat fsnative --longitudinal \
--fs-license-file /licensedir/license.txt --bids-filter-file /licensedir/filtercfg.json

What version of fMRIPrep are you running?

24.0.0

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

effigies commented 4 weeks ago

Does this persist in the latest release?

Blink621 commented 4 weeks ago

Hi, thanks to your reply. I have tried the latest v24.1.1. Surprisingly, the wired fieldmap images disappear. Is this improved by the fix of "Handling of gradient echo fieldmaps is improved" in v24.1.0 ?

However, there are other questions in the latest release. It seems after correction, the parietal and frontal of the brain are darken, with large value in the bottom of the brain. Is this normal? Why was the lower brainstem, cerebellum and orbitofrontal Cortex has so large value comparing to other area?

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