Hi,
Thank you for this quick response. Here's the line for randomise:
randomise_parallel -i all_FA_skeletonised.nii.gz -o oldvsyoung -d design.mat
-t design.con -m mean_FA_mask.nii.gz -n 2000 --T2 -V
I did not use any threshold, I just used the --T2 option. I actually copied
the whole randomise command directly from the TBSS page.
I forgot to tell that I ran this on a cluster. All nodes ran fine and
produced the *SEED* outputs, but not the final files. I had to run the
defragment script manually. It seemed to work fine, as t maps appear OK.
thank you,
Tugan
On Fri, 10 Apr 2009 17:55:36 +0100, Reza Salimi <[log in to unmask]> wrote:
>Hi Tugan,
>could you please send the line which runs *randomise* ?
>Maybe you are using cluster-based inference with a very small
>cluster-forming threshold, which results in a huge significant cluster,
>Cheers
>
>On Fri, Apr 10, 2009 at 5:47 PM, Tugan <[log in to unmask]> wrote:
>
>> Dear all,
>>
>> I am hoping someone can shed a light on what I observed with a data I have
>> been working on. It is a simple set of DTI-FA maps of old and young people
>> and I run TBSS on the data. The data is unbalanced, I have 36 olds and 18
>> youngs. After running randomize, p values (both corrected and uncorrected
>> p-images) are constant 0.99952 almost throughout the whole WM tracts. On
>> the
>> other hand, t-statistics show variance across space, so they look normal.
>> Can anyone speculate why I am getting a fixed p value throughout the entire
>> WM tracts? Moreover, it is the same for both corrected and uncorrected.
>>
>> I browsed through the email discussions but I could not find a similar
>> issue.
>>
>> Thanks in advance for any insights you might have.
>>
>> best,
>>
>> Tugan Muftuler
>>
>
>
>
>--
>G. Salimi-Khorshidi,
>D.Phil. Student, Dept. of Clinical Neurology, University of Oxford.
>[log in to unmask] http://www.fmrib.ox.ac.uk/~reza
>FMRIB Centre, John Radcliffe Hospital,
>Headington, Oxford, OX3 9DU
>Tel: +44 (0) 1865 222466 Fax: +44 (0)1865 222717
>
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