vbthresh

vbthresh thresholds 4D volumes. Any voxel which is below threshold for any time point in the time series is set to zero at all time points. So if you have one blank volume in your time series, vbthresh will zero out all your data. Here's the help text:

VoxBo vbthresh (v1.8.5/Jun 14 2011)
summary: threshold 4D files
usage:
  vbthresh [<flags>...]
flags:
  -i <file>          input 4D filename
  -o <file>          set output filename (default: input filename)
  -c <val>           absolute threshold value
  -b <size>          bin size for histogram thresholding method
  -h                 show help
  -v                 show version
notes:
  The -i argument must be provided.

  Note that if vbthresh finds a value below threshold, it zeroes out
  the entire time series for that voxel.