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Hi Carlos - You seem not to have files called bvals and bvecs in the directory. Where have you put your gradient info? If you call the files "bvals" and "bvecs" in the same directory as "data" then you should be able to run bedpost_datacheck ok, and if this runs through with no errors, you should be able to type cd /home/ccortes/dtidata dtifit -k data -r bvecs -b bvals -m nodif_brain_mask -o dti and this should do the fitting for you. 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 Sun, 24 Oct 2004, Carlos Cortes wrote: > Hi Tim, > Thank You very much for your response/help. I am sorry about the confusion. > > The total volumes I have is 32, I discarded the first volume = ignored scan (for a total of 31). > I have one reference volume and 5 averages of diffusion-weighted scans of 6 directions. > > I have 31 bvals and normalized bvecs > > after running bedpost_datacheck I got: > > > $ bedpost_datacheck ~/dtidata > /home/ccortes/dtidata/data > dim1 128 > dim2 128 > dim3 46 > dim4 7 > datatype 4 > pixdim1 1.8799999952 > pixdim2 1.8799999952 > pixdim3 2.0000000000 > pixdim4 1.0000000000 > cal_max 386.5066 > cal_min -386.5184 > file_type NIFTI-1+ > > /home/ccortes/dtidata/nodif > dim1 128 > dim2 128 > dim3 46 > dim4 1 > datatype 4 > pixdim1 1.8799999952 > pixdim2 1.8799999952 > pixdim3 2.0000000000 > pixdim4 0.0000000000 > cal_max 2000.0000 > cal_min 0.0000 > glmax 2000 > glmin 0 > origin1 0 > origin2 0 > origin3 0 > file_type ANALYZE-7.5 > > /home/ccortes/dtidata/nodif_brain_mask > dim1 128 > dim2 128 > dim3 46 > dim4 1 > datatype 4 > pixdim1 1.8799999952 > pixdim2 1.8799999952 > pixdim3 2.0000000000 > pixdim4 1.0000000000 > cal_max 1.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > num lines in /home/ccortes/dtidata/bvals > cat: /home/ccortes/dtidata/bvals: No such file or directory > 0 > num words in /home/ccortes/dtidata/bvals > cat: /home/ccortes/dtidata/bvals: No such file or directory > 0 > num lines in /home/ccortes/dtidata/bvecs > cat: /home/ccortes/dtidata/bvecs: No such file or directory > 0 > num words in /home/ccortes/dtidata/bvecs > cat: /home/ccortes/dtidata/bvecs: No such file or directory > 0 > cat: /home/ccortes/dtidata/bvals: No such file or directory > cat: /home/ccortes/dtidata/bvecs: No such file or directory > cat: /home/ccortes/dtidata/bvecs: No such file or directory > Runtime error (func=(main), adr=3): Divide by zero > [: 0: unknown operand > number of elements in bvals is not equal to number of vols in data > [: 7: unknown operand > > Any suggestions....please > > Carlos > > >>> [log in to unmask] 10/23/04 10:18AM >>> > 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 > > ------------------------------------------------------------------------------- > > >