Hi - Hima's right, the TFCE option is a lot slower - but then the best
things in life are worth waiting for.....
If your model already contains non-zero-mean EVS (e.g. explicitly
models the groups' means) then you _don't_ need the -D option as you
want to leave the mean in the data.
I would recommend reducing the -n option to say 500 to get a feel for
whether the results are interesting and whether it's worth waiting for
the full 5000 permutations analysis.
We're working on speeding up the TFCE option - hopefully in the next
release it will be faster.
Cheers, Steve.
On 19 Feb 2008, at 03:39, Himachandra Chebrolu wrote:
> Suzanna-
>
> I have used the same command to do my analysis. It has not produced
> any results as it's taking very long than without the -T optin in
> there. What you have on the command line looks fine to me. However I
> would suggest using the -D option to demean the data, use -V for
> verbal info, -v for variance smmothing. These options are not a must
> but my personal preferences and others doing the same stuff can shed
> more light on other options.
>
> You do have to specify "-n 5000" to do 5000 permutations as the
> default is set to 5000. Howver if you want to increase/decrease the
> number of permutations use the -n option.Hope this helps.
>
> Cheers,
> Hima
>
> P.S: My personal expereince has been that with the -T option each
> contrast is taking 3 days to finish 5000 permutations. Without the -
> T option I had each contrast done in 10 hours. I have 100 subjects
> in my analysis. Let me please know if you have similar time
> consumption.
>
> Suzanna Laycock <[log in to unmask]> wrote:
> Hi,
>
> Would someone mind stating the exact command line for running the
> TFCE analysis.
>
> I'm using the following command:
>
> $ randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -
> d design.mat -t design.con -n 5000 -T
>
> Do you need to state the number of permutations, and should that be
> set at 5000?
>
> Thanks
> Suzanna
>
>
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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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