Hi,
On 28 Aug 2009, at 10:31, Mark Rees wrote:
> Hi Steve,
>
> Thanks for the reply. Clustertool should read cluster (but I guess
> you knew
> that) !
>
> A quick question - you suggest the first approach is best and your
> conclusion is right - my corrp image does not have enough
> resolution. Can I
> clarify your suggestion:
>
> Should I re-run randomsie on my original 4D all_FA_skeleotnised or
> do you
> mean I should run it on another file ?
Yes - the same command as before but change the -n option (or add it
if you didn't specify it before) to "-n 1"
And add the "-R" option
You will then get an extra output that is the TFCE-enhanced tstat
image - this is the reason for re-running - because you don't need to
regenerate p-value images you don't need more than 1 permutation. Make
sure you don't overwrite your old p-value images though - set the
output rootname to something new. Then threshold your corrected p-
value image at 0.95, binarise, and use it to make the TFCE image -
then you can look at that in FSLVIew, etc.
Cheers.
>
> Does the "TFCE enhanced tstat output option" you mention equate to --
> T2 or
> another option - I guess its another option I am missing or I would be
> repeating what I have done previously (ie I originally ran --T2
> option on my
> 4d file in order to derive corrp images).
>
> What is the reason for setting the number of permutations to 1 ?
>
> Finally, if I do need to re-run randomise on my 4d
> all_FA_skeletonised file
> again is it worth changing the TFCE height/extent/connectivity
> parameters
> rather than using the defaults built into the --T2 option.
>
> Thanks.
>
> Mark
>
>
>
>
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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