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Hi, I would first check that the identity transformation truly does relate your images. Do this by running flirt: flirt -in diffimage -ref anatomical -init $FSLDIR/etc/flirtsch/ ident.mat -applyxfm -out diff2anat then load diff2anat and anatomical into fslview. If you are happy with this then you can copy $FSLDIR/etc/flirtsch/ident.mat into the place where the diffusion to structural registration file would normally be saved and everything should work from then on. Alternatively, you can use the above flirt command to manually resample masks or other images between the two resolutions (in either direction). Remember to rethreshold and binarise your mask image after transformation, as voxels may only partly overlap and hence generate values between 0 and 1. All the best, Mark On 23 Feb 2008, at 14:32, Roman Loonis wrote: > Yeah I understand that. So does that mean if two images which are > already registered, but have two different resolutions, are > considered in the same space for probtrackx? How can I get a mask > on one be the same on the other despite the reduction in resolution? > > Thank you, > Roman > > On Sat, Feb 23, 2008 at 2:24 AM, Steve Smith <[log in to unmask]> > wrote: > Hi - it doesn't quite work like that. If you use the registration part > of the FDT GUI then the transform between diffusion and structural > data will get computed and saved. > > Then when you specify a mask in structural space you just tell FDT > that this is the space it's in, and it will use the appropriate > transform for you, when running the tractography. > > Cheers. > > > > On 21 Feb 2008, at 19:08, Roman Loonis wrote: > > > I have already registered my images (the anatomical to the diffusion > > data) prior to using bedpostx > > and I have modified correspondingly the resulting changes in the > > vector directions for my bvecs file. > > I had to do so because I am looking at monkey diffusion data. My > > question is the following... > > Although the files are properly registered and therefore need no > > transformation file, they still have > > different resolutions. When I input my masks which I have drawn on > > the anatomical, do I need to > > indicate in probtrackx that the seed space is not the diffusion > > space? How can I make sure that there > > is a proper translation of the higher resolution mask into a lower > > resolution one? > > > > > ---------------------------------------------------------------------- > ----- > 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 > ---------------------------------------------------------------------- > ----- >