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