First of all if placed in /usr/local/wfu_pickatlas it should be found, so I wonder if you are using a version that is too new for what BioImage Suite was coded to look for. (If need be I can zip the one we have).

BioImage Suite looks for a folder MNI_atlas_templates which should be inside /usr/local/wfu_pickatlas

If it finds that then it looks for files such as TD_lobe.hdr inside that. We have not tested with recent versions so the filenames may have changed.

Xenios