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
> >
>
>
