Hi,
Could you upload your input files ( and details of the exact
command line call ) to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
let me know the 6-digit reference number, and we'll have a look what's
going wrong?
Many Regards
Matthew
> Hi,
>
> Thank you all for your valuable insights. I just had a chance to go
> back and
> try more things. It looks like it is not related to the computer
> cluster and
> parallelization. I did two things:
>
> 1) I ran it again on the cluster and looked at each *SEED_tfce_p
> and*SEED_tfce_corrp images. They all have constant p values in maybe
> 90% of
> the tracts. All p values are 0.993333.
>
> 2) I ran it on a single computer using standard randomise command
> (without
> parallelization). Again, all p values are fixed at 0.99875.
>
> So, would you think that tfce is mishandling this? Both corrected and
> uncorrected p values have the same maps. What would I lose/gain if I
> run it
> without tfce?
>
> kind regards,
>
> Tugan
>
>
>
> On Sat, 11 Apr 2009 08:59:13 +0100, Steve Smith
> <[log in to unmask]> wrote:
>
>> Yes - sounds like something's gone wrong - with the TFCE option I
>> wouldn't expect you to get the same p-values everywhere.
>> If the SGE scripts didn't finish the cluster job on their own then at
>> the least something's wrong with the cluster setup - I would suggest
>> asking your sysad to look into why it didn't finish.
>> Cheers.
>>
>>
>> On 10 Apr 2009, at 23:40, Tugan wrote:
>>
>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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