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

1

Hello,

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.

Capture1.PNG
Capture1.PNG1946×832 302 KB

Capture2.PNG
Capture2.PNG2005×822 331 KB

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

Best,

George

2

Hi,

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

Best,
Steven

3

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,

George