Issue with antsBrainExtraction.sh using fmriprep

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1

Hello,

After running fmriprep on 10 subjects, 4 of the brain extractions failed and I am unsure of how to troubleshoot this issue (example included). Of note, our anatomical data are PURE corrected. Would that be redundant or cause an issue with the N4BiasField correction?

cmd="${SINGULARITY_CMD}
–participant-label $subject
–ignore fieldmaps slicetiming
–bids-filter-file /data/sen.json
–fs-license-file /data/derivatives/license.txt
–fs-subjects-dir /data/derivatives/T1
–fs-no-reconall
–bold2t1w-dof 6 --nthreads 8 --omp-nthreads 8
–work-dir /work
–write-graph --notrack -v
/data/nifti_test /data/derivatives/FMRI_Sentences participant"

Version 21.0.1

Screen Shot 2022-03-08 at 11.44.28 AM
Screen Shot 2022-03-08 at 11.44.28 AM1697×762 469 KB

Thank you.

2

Hi, it is difficult to see but it seems to me that the contrast between WM and GM seems very low in this image, and also the SNR. Did you try with another software (such as BET from FSL) to see if you get a better brain extraction? If you manage to get a good brain extraction from outside FMRIPREP, you may feed it to FMRIPREP with the option –skull-strip-t1w skip .

I have no experience with PURE but from my experience with PreScan Normalize from Siemens, it is not incompatible with N4.