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Hi - you should run FLIRT on the brain-extracted T1 image, not the outputs of the segmentation; save the FLIRT transform, and then apply that transform to the segmentation outputs. Cheers. On 1 Feb 2012, at 08:01, Fellhauer, Iven wrote: > Hi Steve, > > thanks for your answer. I think that I need the -g option with fast to get seperate image files for each segmentation class. If I activate this option I get several files and I am not sure which files should I pass to flirt? > > Best regards, > > Iven Fellhauer > > ________________________________ > Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag von "Stephen Smith [[log in to unmask]] > Gesendet: Dienstag, 31. Januar 2012 15:02 > Bis: [log in to unmask] > Betreff: Re: [FSL] Segmentation Workflow > > Hi - no, do fast before FLIRT, to avoid interpolation of the images fed into the segmentation. > Steve. > > > On 31 Jan 2012, at 13:56, Fellhauer, Iven wrote: > > Dear colleagues, > > > > I want to segment T1-Images into GM, WM and CSF. Now I am not sure in which order should I execute the fsl tools and if the submitted parameters are sufficient. > > > > My Workflow > > 1. bet <input image> <output image> -R -S -B > > 2. flirt <input image == output image bet> -ref ..../MIN152_T1_1mm <output image> > > 3. fast <input image == output image flirt> > > > > Is this workflow okay? Is there a script that automates the steps? > > > > Best regards, > > > > Iven Fellhauer > > > > --------------------------------------------------------------------------- > 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]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------