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
> -------------------------------------------------------------------------------
>
