Question about "min_coverage" flag in xcp-d

Software Support
1

Greetings,

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?

2

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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