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Hi, Qasim. If you type fslmaths at the command line it will show you all the things it can do (a lot!). It can certainly be used for spatial smoothing (see kernel) and bandpass filtering (see -bptf). Best, Paul On Thu, Jun 27, 2013 at 2:42 PM, Qasim Bukhari <[log in to unmask]>wrote: > Dear all, > I m trying to do all the pre processing using the command line and I have > different some scripts for that. However I m not entirely sure of the > pre-processing pipeline. Is it like this as below ? > > mcflirt (EPI time series motion correction) > flirt (registration of functional to anatomical) > spatial smoothing > intensity normalization > highpass filtering > melodic > > Can I skip high pass filtering (or any other of the previous steps) if I > do melodic ? > I also couldnt find specific commands for spatial smoothign or highpass > filtering; do I have to use fslmaths to do these ? can somebody please tell > the detailed options ? > > If I try using GUI for any ONE of these tasks; I cannot disable the rest > of the options. Is there some way to do that ? > > Thanks a lot > best > Qasim > > > Qasim Bukhari > > Research Assistant and Doctoral Candidate > > Institute for Biomedical Engineering > > ETH and University Zurich > > Wolfgang-Pauli-Strasse 27, HIT E22 > > webpages: MR-page <http://www.mr.ethz.ch/ibt/?name=sbukhari> > > http://www.biomed.ee.ethz.ch/people/sybukhar > > > >