Dear Experts,
I have a short question regarding the use of the Melodic command line.
I am attempting to perform group ICA on my resting-state data following the example in the ICA practical (https://open.win.ox.ac.uk/pages/fslcourse/practicals/ica/index.html#dim).
I noticed that the command used here included the --nobet option but did not include a --bgthreshold option.
melodic -i input_files.txt -o groupICA15 \
--tr=0.72 --nobet -a concat \
-m $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask.nii.gz \
--report --Oall -d 15
From melodic --help, I got the impression that the --bgthreshold is needed if --nobet is used:
"--bgthreshold brain / non-brain threshold (only if --nobet selected)"
Is there a special reason why the --bgthreshold is not defined in this example, or is there some kind of automated calculation of the threshold?
Thanks a lot for the clarification!
All the best,
Madeleine
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