Dear Kangjoo,

Sorry for the late answer. We have observed such high failure rate for data where the voxel-to-world information in the header is either lost or compromised, and consequently the functional/anat volumes are completely misrealigned in native space. A quick fix is to set:
opt.slice_timing.flag_center = 1;

You may also have to do some centering "surgery" on the anatomical scans themselves. Please have a look at the QC&QA manual
http://www.nitrc.org/frs/download.php/72...

Best,

Pierre