Issue with preprocessed T1 and segmentation


I am running fmriprep 20.0.5 through singularity. Subjects completed preprocessing successfully, however in checking the summary htmls I am seeing that some subjects have poor T1 segmentation. It seems like the issue is in the creation of the preprocessed T1 from the T1 image and the inplane T1. I am attaching screenshots of each. I don’t see any immediately obvious differences in the T1 images for the subjects where the segmentation worked well and for those where it did not. Is this any issue with INU correction? Any potential solutions? Any help is appreciated!


This is the code used:

singularity run --cleanenv $PI_HOME/fmriprep/fmriprep-20.0.5.simg $PI_HOME/BIDS_data $PI_HOME/analysis/fmriprep participant --participant-label xx -w $PI_SCRATCH/work --omp-nthreads 8 --nthreads 12 --mem_mb 30000 --use-aroma --fs-license-file $PI_HOME/freesurfer/license.txt