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I'm not sure if there's more you should be doing, but you shouldn't be using the dti_FA image in FLIRT to get the str2diff.mat. Instead you should be using the nodif_brain image. Not sure if that will solve your problem but it might help. Good luck! Kristen -----Original Message----- From: FSL - FMRIB's Software Library on behalf of Ravi Shetty Sent: Mon 4/7/2008 4:40 AM To: [log in to unmask] Subject: Re: [FSL] T1 and DTI Registration problems Sorry I am not sure if I quite follow. I have been registering my diffusion data(dti_FA) to the reference image(T1 weighted) and I believe that would give me the equivalent of the str2diff.mat. From there I use that matrix to convert the ROI mask I created on my T1 weighted image into diffusion space. I then overlay that new diffusion space ROI mask onto my original diffusion image and see if the images are being registered correctly. I use this method to check because the images outputed after registration always seem to line up pretty well but once I run probtrackx my results were very off. This just seemed a faster way to check the registrations accuracy. Please let me know if I seem to be missing a step. Thanks. On Mon, 7 Apr 2008 08:33:21 +0100, Steve Smith <[log in to unmask]> wrote: >Just a quick sanity check - you _are_ inverting the DTI->structural >transform before using it to transform structural-space ROIs back to >DTI space? >Cheers. > > >On 7 Apr 2008, at 03:03, Ravi Shetty wrote: >> Hi I have been using FLIRT to register my T1 and DTI images to each >> other but keep running into >> problems. The registered images produced are always very close to >> what they should be when I >> overlay them onto the T1 image. The problem I have is the matrixes >> don't always reflect the >> registration image. I create a CC ROI mask on the T1 image/ >> registered image and use the matrix I >> produced to convert it back into difusion space. Now when I do this >> with some subjects the ROI will >> be spot on the CC and for others it will be off somewhere in the >> cortex or even just into the black >> void. I can't seem to find any rhyme or reason for this and the >> variation of how off the matrix is does >> not seem to be consistent, any help figuring this out would be >> appreciated. Thanks. >> > > >--------------------------------------------------------------------------- >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 >--------------------------------------------------------------------------- >=========================================================================