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Hi - you can just delete the scans from the raw 4D images using fslroi. Cheers. On 20 Jan 2009, at 16:24, Yael Shani wrote: > Hi > I have a question about dummy scans. > The fMRI machine we are working with has some kind of a bug- > When a run begins, instead of creating dummy scans and then start > sending the signal to the subject, the signal starts immediately (At > time zero), however, the fMRI does not record the activation of the > first few seconds (For example, if I use Tr 3, then for the first 6 > seconds it will not record the activation). > for example, if the run is 72 trs, then the subject will see the > signal from time zero, the fMRI will start recording after 6 > seconds, after70 trs the subject will stop receiving a signal and > the fmri will record additional 2 trs. > So we designed the protocol in a way that we subtract 6 seconds from > all the times recorded. > The problem is the end of the run - the fMRI records 6 seconds more > after the signal ends. > I wanted to know how should I treat these last seconds in FSL. Is > there a way to define it as dummy scans? > Many thanks > Yael --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------