Question about "min_coverage" flag in xcp-d


I’m puzzled by the --min_coverage flag in XCP-D.

–min_coverage, --min-coverage

Coverage threshold to apply to parcels in each atlas. Any parcels with lower coverage than the threshold will be replaced with NaNs. Must be a value between zero and one, indicating proportion of the parcel. Default is 0.5.

Default: 0.5

So if parcel of a given atlas contains 20 voxels, if one of my participants BOLD response is nil/non-existant in more than 10 of those voxels than I will see NaN in the output.
My question is how is non-activity defined for this purpose? NaN values throughout the run or any flat value throughout the run? If there is even 1 TR worth of signal does it become an “active” voxel?

In the case of NIfTIs, we just use the brain mask from the preprocessing pipeline, so it really depends on how the preprocessing pipeline defines non-activity.

For CIFTIs, vertices are flagged if the full time series is composed of zeros and/or NaNs. In that case, yes, if there’s even 1 TR of signal it will be treated as an active vertex.

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