Fmriprep T1 Segmentation improvement

[syoun]

Summary of what happened:

My fMRIPrep result for T1ws segementation was able to get the most of the brain, but it is not able to capture the whole brain especially towards the top of the brain. I have confirmed that this has happened to both of our scanned participants.

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

/opt/conda/envs/fmriprep/bin/fmriprep /scratch/user/bids/ /scratch/user/fmriprep participant --participant-label sub-001 --fs-license-file /scratch/user/license.txt --ignore slicetiming --me-output-echos --me-t2s-fit-method curvefit --nthreads 16 --omp-nthreads 16

Version:

• fMRIPrep version: 23.1.4

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

• Singularity

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

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

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[syoun]

Hello, trying to see if I can get some ideas on how to improve this. It definetly looks like the top of the brain is “cut off” because the brain tissue is way too dark. I have tried manually creating a mask, but I am still having some issues keeping the whole brain.

Any help would be much helpful. Thank you!