>>>
[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
> >
-------------------------------------------------------------------------------
>
>
>