I did have same problem. Initially, I didn't realize that my problem was in concat_bvars step. Make sure you the concatenated bvars file is good (e.g. at least some KB in size, also check "NumberOfSubjects" field at the 3rd line of [structure]_all.bvars file - it should be equal to the number of your input files supplied to concat_bvars command).
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Gajendra Jung Katuwal
PhD Candidate in Imaging Science
Carlson Center for Imaging Science, RIT
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