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You can use flirt from the command line (or the ApplyXFM GUI) to apply the str2diff.mat transform to e.g., the T1-weighted image and your masks and create output files that are these images in diff space. Then open the nodif image in fslview and add your transformed images to check that structures of interest are correctly registered. Heidi On 8 Dec 2005, at 21:45, Kristen Lindgren wrote: > Great, thanks! Sorry, one more question. Once the registration is > done, how can you view it to make sure it's ok? I can't find any > additional files that are created to view in fslview and I can't > view the transforms in fslview. Thanks! > > > > Kristen > > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Heidi Johansen-Berg > Sent: Thursday, December 08, 2005 4:39 PM > To: [log in to unmask] > Subject: Re: [FSL] Using FLIRT to align DTI and T1 images > > > > If your seed masks are in structural (T1) space then you should > enter the str2diff.mat as the transformation in probtrack. > > Heidi > > On 8 Dec 2005, at 21:36, Kristen Lindgren wrote: > > > > Ok, I think I understand. I used the Registration tab in FDT and that > > created diff2str.mat and str2diff.mat. So is this what I should > enter in > > ProbTrack? > > > > Bedpost directory - bedpost directory for subject > > Seed Space Mask Image 1 and 2 - files for masks that I created > > Select Seed Space is not diffusion > > Diff-space transform - enter diff2str.mat file that was just created > > > > Thanks for your help! > > > > Kristen > > > > > > Heidi Johansen-Berg FMRIB Centre John Radcliffe Hospital Headington, Oxford OX3 9DU, UK Tel: +44 (0) 1865 222782 Fax: +44 (0) 1865 222717 [log in to unmask] http://www.fmrib.ox.ac.uk/~heidi