fMRIprep N4BiasFieldCorrection Failure

Hi fMRIprep users,

I am trying to preprocess the openly available Balloon Analog Risk-Taking Task dataset available from OpenNeuro.

I have found that for one of the subjects, sub-04, preprocessing is failing. It seems as if the N4BiasFieldCorrection applied to the anatomical T1 image as part of the pipeline is actually inducing dropout at the front of the brain:

Left is the raw sub-04_T1w.nii.gz image, right is the sub-04_desc-preproc_T1w.nii.gz. As far as I’m aware the only difference between these images is that ANT’s N4BiasFieldCorrection has been applied to the right. This is subsequently causing skull-stripping to fail (brain mask it too small), and then registration to fail. Preprocessing is successful for all other subjects in the dataset.

I was wondering if it is possible to remove the N4BiasFieldCorrection from the pipeline, or if any other solutions exist? I have tried using the --force-bbr argument as was suggested here but the problem persisted.

I am running fMRIprep v1.5.1through singularity, here is the complete command:
/usr/local/miniconda/bin/fmriprep /well/nichols/users/bas627/BIDS_Data/RESULTS/SC2/data/raw/ds001_R2.0.4 /well/nichols/users/bas627/BIDS_Data/RESULTS/SC2/data/processed/ds001 participant --participant-label 04 --ignore slicetiming --fs-license-file /well/nichols/users/bas627/BIDS_Data/RESULTS/SC2/license.txt --fs-no-reconall -w /well/nichols/users/bas627/BIDS_Data/RESULTS/SC2/data/processed/ds001/ds001_sub-04_work --mem-mb 13000 --low-mem --resource-monitor --nthreads 4 -vvv

I am happy to provide more info if necessary. Thank you!


Hi Alex, I am having the same issue, did you ever figure out a solution? Thank you!

Hi @arwang , sorry for taking a while to get back to you. We could not fix the intensity problems with this subject so we ended up having to drop it. It’s notable, however, that our raw T1w image for this subject was already pretty screwed up, and had some insanely high-intensity regions.

If this isn’t the case for you, and your issues are with the segmentation or registration, then my question would be if you are disabling the freesurfer processing or not? Initially, I had the FS processing disabled, and for some other subjects, I had a bad segmentation and registration. I found enabling FS processing helped a lot here.