Hi Yi-Shin,
Thanks for sharing your experience. What confused me is that the p values
were fixed at 0.99952. So, in the p-value images it is either 0 or 0.99952;
no other values in the entire image. And it is the same both in corrected
and uncorrected. I had analyzed other data from other populations before and
I had quite a range of p-values and they usually drop after FWE correction.
best,
Tugan
On Fri, 10 Apr 2009 18:16:34 -0400, Yi-Shin Sheu <[log in to unmask]>
wrote:
>Hi Tugan,
>
>Did you check the subject's FA skeleton in each group (young versus old)?
>
>For example, in the same area/voxel, does your FA skeleton appear to be
>uniformly higher/lower in the young group across the whole skeleton compared
>to the old group? Not necessary all subjects in the same group were that
>way, maybe just a few subjects have distinctively different FA value could
>cause the problem you described (significant p value across whole
>skeleton). Maybe you could make a testing ROI and extract the FA value from
>each subject's skeleton so that you can take a better look quantitatively.
>
>I asked you this because I have experienced similar problem recently.
>
>Yi-Shin
>
>----
>Yi-Shin Sheu
>Research Assistant
>Developmental Biopsychiatry Research Program
>McLean Hospital / Harvard Medical School
>115 Mill Street
>Belmont, MA 02478
>Tel: 617-855-2942
>Fax: 617-855-3712
>
>
>On Fri, Apr 10, 2009 at 2:28 PM, Tugan <[log in to unmask]> wrote:
>
>> 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<http://www.fmrib.ox.ac.uk/%7Ereza>
>> >FMRIB Centre, John Radcliffe Hospital,
>> >Headington, Oxford, OX3 9DU
>> >Tel: +44 (0) 1865 222466 Fax: +44 (0)1865 222717
>> >
>>
>>
>
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