Brain mask not correct in one run but correct in another run


I am quality checking my data and I have found that for 1 subject the brain masks are not correct and have a weird shape. The segmentation of the anatomicals is working perfectly and the brain mask is only peculiar for one of the 2 runs of my study.

  • fMRIPrep command: /opt/conda/bin/fmriprep /data /out participant --participant-label 06 --fs-no-reconall --nthreads 8 --omp-nthreads 4 --mem-mb 32000 --low-mem --dummy-scans 6 --use-aroma
  • fMRIPrep version: 21.0.0

Here is the data from the SDC.

Would anyone have any suggestions on how to fix this issue?




Do the T1 images have decent tissue contrast, and have you tried using FreeSurfer in the fMRIPrep workflow?


Thanks for the fast reply.

The T1w have good contrast upon visual inspection. In terms of FreeSurfer, I have run the analysis of all the other subjects without it in order to save time in the analysis. Each participant takes around a day to complete the preprocessing due to the included ICA-AROMA and a big run time for my functionals. As a result I am a bit hesitant to rerun all my participants with FreeSurfer included.

Also may I ask why would the FreeSurfer help with this issue? For clarification the experiment has 2 runs (each using the same structural for registration). Why would only the second run have this issue but not the first one?

I will try to run the analysis with the Freesurfer included though I was just wondering if there is an alternative where I do not need to reanalyse all subjects (instead just adjusting the specific one).

In any case thanks again for your help,