Hello! I am very new to fmriprep so forgive me if I am asking a silly question. I have run:
fmriprep ${sourcedata} ${outputdata} participant -w{work} --participant-label ${sub_idx} -t rest --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym anat func --use-aroma --t2s-coreg --write-graph --stop-on-first-crash --nthreads 4 --omp-nthreads 4 --mem_mb 20480 -vvv --fs-license-file ${fs-license}
The ouput is fine and no errors were reported… but for every subject the spatial normalisation of the T1w image to the MNI152NLin6Asym template it is missing the z = 12 slice (please see attached screenshot). Is there a obvious reason for this I am missing?
Any help is appreciated and thanks in advance 
