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Carlos - Your report below suggests you have 1 reference volume followed by 6 averages of 6 directions. This would make 1+6x6=37 volumes. The bvecs/bvcals you attached each have 31 entries, and your next email says your data contains 32 volumes. I am not entirely surprised things aren't working too well!! Rule 1 of FDT is that you need the same number of entries in the gradient files as in the data. You can check this using bedpost_datacheck I don't know exactly what has happened here, but I suspect the following: 1) You have included the "ignored scan" in your data - if so, remove it. 2) You have only got 5 averages of the diffusion-weighted scans. Then the number of elements in the bvecs/bvals and the number of volumes in data are all 31. 3) The bvecs you sent are not normalised. You should normalise them (make sure all vectors have magnitude=1 (x,y,z)=(x,y,z)/sqrt(x^2+y^2+z^2) ) Then you should be good to go. T ------------------------------------------------------------------------------- Tim Behrens Centre for Functional MRI of the Brain The John Radcliffe Hospital Headley Way Oxford OX3 9DU Oxford University Work 01865 222782 Mobile 07980 884537 ------------------------------------------------------------------------------- On Thu, 21 Oct 2004, Carlos Cortes wrote: > Hi Tim, > > Thank You for the suggestion. This is what I get from the physics Team: > > b=1000 for all gradients. A DTI image consists of a number of concatenated > 128x128x46 sub-images as follows: > > Sub-image 1 = ignored image > Sub-image 2 = reference grad direction = (0,0,0) > Sub-image 3 = grad 1 direction (1 0 1) > Sub-image 4 = grad 2 direction (-1 0 1) > Sub-image 5 = grad 3 direction (0 1 1) > Sub-image 6 = grad 4 direction (0 1 -1) > Sub-image 7 = grad 5 direction (1 1 0) > Sub-image 8 = grad 6 direction (-1 1 0) > ... > > Sub-images 3-8 are repeated, in the above order, 5 more times. Thus, to get > the DTI corresponding to the first gradient of (1 0 1), you'd average > sub-images 3, 9, 15, 21, and 27, for the second (-1 0 1) gradient, you'd > average sub-images 4, 10, 16, 22, and 28, etc... > > Attached are the files I created, but I'm not sure if they are correct. > I put 0.0 for the reference image, but Do I have to add values for the ignored image? > > suggestions???? > > Thanks!!!! > Carlos > > > >>> [log in to unmask] 10/18/04 04:39AM >>> > Hi there - > > To run FDT, you need to know the gradient directions, and b-values applied > during the diffusion weighted scan. These can be computed from the > gradient profiles used during the acquisition. Most modern scanners will > output these values but, if not, you should ask your physics team to > provide you with them. > > For info on how you input them into FDT, see > > http://www.fmrib.ox.ac.uk/fsl/fdt/index.html > > T > > > On Sun, 17 Oct 2004, Carlos R. Cortes wrote: > > > Hello, > > I'm completely new to DTI and not to much experience using fsl. I have a > > couple of questions (sorry if they are too basic). > > 1. What are the parameters I have to know about DTI data in order to use > > FDT? > > 2. How can I obtain the bvals and bvecs files? > > Thanks for the tool, > > Carlos > > > > -- > ------------------------------------------------------------------------------- > Tim Behrens > Centre for Functional MRI of the Brain > The John Radcliffe Hospital > Headley Way Oxford OX3 9DU > Oxford University > Work 01865 222782 > Mobile 07980 884537 > ------------------------------------------------------------------------------- >