I think I deleted all the .msf files also. I think you will be better off deleting all the files in the FAi folder other than the scaled FA images from the tbss_1_preproc step. I am not sure if there is a more efficient way, but that was what I did. Cheers, Hima Cherif Sahyoun <[log in to unmask]> wrote: Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp files? it would be a shame to restart from scratch... On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> wrote: I had the same problem. After much pain, I found that the .commands file will be deleted if you already have files from the tbss_2_reg which was run earlier. So I deleted all the old files in the FAi directory and then reran the tbss_2_reg and everything seems to work fine. Hope this helps. Cheers, Hima Cherif Sahyoun <[log in to unmask]> wrote: Hi, I have run tbss_2_reg -n when it appeared to be done I went ahead with tbss_3_postreg -S and got a series of errors (not finding certain header files). So I went back to look into the directory and indeed it seems tbss_2 exited prematurely. I tried to re-run it to pick up where it left off, but now got: wc: .commands: No such file or directory 28980 Any thoughts? Thanks, cherif --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. -- ------------------------------------------------------------------------------------------ Cherif P. Sahyoun HST-MEMP Developmental Neuroimaging of Cognitive Functions C: 617 688 8048 H: 617 424 6956 [log in to unmask] "Live as if this were your last day. Learn as if you'll live forever" Ghandi ------------------------------------------------------------------------------------------- --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.