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