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Well it looks as though the issue was the motion correction. We used 4 shot EPI and ended up with quite a bit of ghosting. When I turn off the motion correction it doesn't matter if I delete volumes, and the resulting image looks a lot more like the input images. Looks like I might have to find another correction method, or get some better images. Thanks for all the help! Barry > There shouldn't be any negative values in the data, and as far as I can > tell there aren't any. I'm looking at hummingbird brains so would the > scale be an issue for some reason? How is the brightness threshold > figured out? > > Barry > > > >> Hi - I've not seen this before - is it possible that your data includes >> negative values? We don't generally expect to see that so that could >> cause >> problems. I would recommend fixing that one way or another before >> feeding >> timeseries data into analyses… >> >> Cheers. >> >> >> On 21 Jan 2013, at 23:30, Barry Bohnet wrote: >> >>> I went throught the log trying to figure out where the problem lies, >>> and >>> it seems that I keep running into trouble with Susan. It seems that >>> depending on the number of volumes I delete, the input value for the >>> brightness threshold is negative. Whenever the brightness threshold in >>> Susan is negative I recieve the error message "Cannot open volume >>> prefilitered_func_data_smooth for reading!" after runnning fslmaths on >>> prefiltered_func_data_smooth. How is the brightness threshold >>> calculated? Could this be a problem with whatever the first loaded >>> volume is? >>> >>> Any help is appreciated! >>> >>> >>> Barry >>> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> --------------------------------------------------------------------------- >> >> >> >> > >