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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