Hi-

What was the 3dNetcorr command that you entered? An example one would be:

3dNetCorr                                  \
         -inset TIME_SERIES_DSET               \
         -in_rois ROI_MAP_DSET              \
         -mask MASK_DSET                     \
         -prefix OUTPUT_DSET

where there are two main inputs:
+ a TIME_SERIES_DSET, which is a 3D+time dataset of time series values throughout a volume,
+ a ROI_MAP_DSET, which is a map of ROIs (each ROI is a set of voxels with the same integer value, whether contiguous or not),
and a secondary/optional input, the MASK_DSET (a mask to apply to further restrict the volume analyzed, if you want).

It sounds like you have made the ROI_MAP_DSET already from using 3dUndump (and you should use the AFNI GUI to verify that the spheres are in the places you want).

Where is your TIME_SERIES_DSET coming from?

--pt