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Hi Steve, I thought I create them like that, I got confused with my Windows set up that only show the name without the extension. Thanks !!!! Carlos >>> [log in to unmask] 10/24/04 12:16PM >>> Carlos - the files should not have the .txt extension - see the manual pages! Steve. On Sun, 24 Oct 2004, Carlos Cortes wrote: > Hi Tim, > Thanks, I have them in the same directory, > > ~/dtidata > $ ls -l > total 17409 > -rwxrwxrwx 1 Administ None 153 Oct 24 11:00 bvals.txt > -rwxrwxrwx 1 Administ None 504 Oct 24 10:59 bvecs.txt > -rwxr--r-- 1 ccortes None 8381314 Oct 24 09:17 dat.nii.gz > -rw-r--r-- 1 ccortes None 1358 Oct 24 09:21 data.ecclog > -rwxr--r-- 1 ccortes None 7921014 Oct 24 09:21 data.nii.gz > -rwxrwxrwx 1 Administ None 348 Oct 22 22:03 nodif.hdr > -rwxrwxrwx 1 Administ None 1507328 Oct 22 22:03 nodif.img > -rwxrw-rw- 1 ccortes None 10685 Oct 23 14:46 nodif_brain_mask.nii.gz > > Carlos > > > > >>> [log in to unmask] 10/24/04 12:07PM >>> > 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 > > > ------------------------------------------------------------------------------- > > > > > > -- Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve