Good news!
With a bit of fiddling, you can usually make bet perform well. Usually you
will only have to optimise the bet parameters once for your acquisition
scheme, and use the same parameters for each image acquired in the same
way.
I usually use "-f 0.4" with diffusion weighted scans acquired in Oxford.
However, if you are finding it very hard to tune bet, you can use a binary
mask generated by any program. Alternatively, if you are just using
dtifit, and not doing tractography, you can just use an image full of
ones. Then dtifit will process every voxel in the image.
Hope this is useful
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, 17 Oct 2004, Jay Ives wrote:
> Tim,
>
> Brilliant! Great colourful images now, thanks.
>
> BTW, I find that BET doesn't work _perfectly_, and the step of making the
> binary mask is a bit of a pain. Other software I've tried use a threshold to
> mask off non-brain tissues. Could FDT possibly make such a capability
> available?
>
> Thanks
>
> J
>
> ----- Original Message -----
> From: "Tim Behrens" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Sunday, October 17, 2004 4:38 PM
> Subject: Re: [FSL] DTIFit
>
>
> > Hi there -
> >
> > On Sun, 17 Oct 2004, Jay Ives wrote:
> > >
> > > Can someone tell me how to fill in the bvecs file correctly? The
> > > information I have about the gradient directions in the 30 b direction
> > > sequence I am using shows x, y, and z the absolute values of which add
> up
> > > to one as in the exerpt below.....
> > >
> > > 1 0.4356 -0.226576 -0.770884 0.004225 0.734449
> > > 0 0.564001 0.343396 0.145161 0.613089 0.112896
> > > 0 0 0.430336 0.0841 -0.381924 -0.152881
> > >
> >
> >
> > No this is not quite right. You need to normalise each gradient direction
> > such that its _magnitude_ is equal to 1.
> >
> > To do this, for each gradient direction, r, compute
> >
> > r_norm=r/sqrt( r(1)^2+r(2)^2+r(3)^2 );
> >
> > This is not the same as ensuring that the sum of absolute values in the
> > vector is equal to 1.
> >
> > > I get a good FA map with these, but the V1_RGB looks very smearedn and
> the
> > > colours are mostly pretty pastels, rather than good strong blue, green,
> > > and red.
> >
> > This is because the display range in fslview is set wrong. If you
> > set it as 0->1 you will get nice looking strong primary colours.
> >
> > I'm not sure about the TCL error in the GUI - we'll look into that next
> > week.
> >
> >
> > Hope this helps
> >
> > Tim
> >
> >
> > >
> > > Also, I can run the tools from a command line , but I get an error if I
> > > try to use the GUI. Here is the message.....
> > >
> > > bad cursor spec " watch red white "
> > > bad cursor spec " watch red white "
> > > (processing "-cursor" option)
> > > invoked from within
> > > "$w configure -cursor { watch red white } "
> > > (procedure "fdt_monitor" line 5)
> > > invoked from within
> > > "fdt_monitor $w "${FSLDIR}/bin/eddy_correct $eddy(input) $eddy(output)
> > > $eddy(refnum)""
> > > ("eddy_current" arm line 18)
> > > invoked from within
> > > "switch -- $tool {
> > > eddy_current {
> > > global eddy
> > >
> > > set errorStr ""
> > > if { $eddy(input) == "" } { set errorStr "You need to specify
> > > the input ..."
> > > (procedure "fdt:apply" line 7)
> > > invoked from within
> > > "fdt:apply .fdt keep"
> > > invoked from within
> > > ".fdt.apply invoke"
> > > ("uplevel" body line 1)
> > > invoked from within
> > > "uplevel #0 [list $w invoke]"
> > > (procedure "tkButtonUp" line 9)
> > > invoked from within
> > > "tkButtonUp .fdt.apply
> > > "
> > > (command bound to event)
> > >
> > > Thanks for this great tool and any assistance you can offer to get me up
> > > and running.
> > >
> > > J
> > >
> >
> >
>
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