Hi,
On 18 Feb 2009, at 00:42, Michael Scheel wrote:
> Hi Steve,
>
> the design matrix was an example for a paired t-test of 5 people (to
> make the matrix shorter - i changed the matrix, but stick to the
> example with 5 and hope now it makes more sense and that is indeed
> the correct design.matrix).
> And yes - the answer to the previous FLAME contrast-of-contrast
> question did clarify the situation a bit. However, maybe let me try
> to rephrase:
>
> I assume that negative numbers in the output from siena
> (A_to_B_flow.nii.gz) mean that there has been atrophy in this
> region, while positive mean that growth occured.
> >siena_flow2std A B< just transforms these into standard space (and
> keeps the meaning of negative numbers being atrophy and positive
> being growth).
correct
> Now if I test for differences between the drug and the placebo
> condition with this design matrix and contrasts.
>
> Input Group EV1 EV2 EV3 EV4 EV5 EV6
> s1_prepost_drug 1 1 1 0 0 0 0
> s2_prepost_drug 1 1 0 1 0 0 0
> s3_prepost_drug 1 1 0 0 1 0 0
> s4_prepost_drug 1 1 0 0 0 1 0
> s5_prepost_drug 1 1 0 0 0 0 1
> s1_prepost_plac 1 -1 1 0 0 0 0
> s2_prepost_plac 1 -1 0 1 0 0 0
> s3_prepost_plac 1 -1 0 0 1 0 0
> s4_prepost_plac 1 -1 0 0 0 1 0
> s5_prepost_plac 1 -1 0 0 0 0 1
>
> Contrasts
> EV1 EV2 EV3 EV4 EV5 EV6
> Condition A>B 1 0 0 0 0 0
> Condition B>A -1 0 0 0 0 0
>
> So my understanding is that Contrast_1 (Condition A>B) is asking for
> where has more growth (or less atrophy) happened during the drug
> condition compared to placebo?
> And Contrast_2 (Condition B>A) is asking the same thing for the
> placebo condition compared to the drug condition?
>
> Is my interpretation right? Thanks a lot, Michael
That's right - and you can look at the separate pre- or post- group
mean effects (though not using this model!) to help disambiguate what
those contrasts are saying.
Cheers.
>
>
> On 17-Feb-09, at 12:50 AM, Steve Smith wrote:
>
>> Hi,
>>
>> It's not clear how your design relates to your "20" drug/placebo
>> timepoints - however maybe this is answered by my previous email,
>> about FMRI contrasts-of-contrasts?
>>
>> Cheers.
>>
>>
>> On 17 Feb 2009, at 00:27, Michael Scheel wrote:
>>
>>> Dear fsl experts,
>>>
>>> I have a question regarding the output of siena. We scanned 20
>>> subjects at four different timepoints - 1) PreDrug 2) PostDrug
>>> 3)PrePlacebo 4) PostPlacebo.
>>> I used siena to estimate atrophy/growth in both conditions (Placebo
>>> and Drug) individually
>>>
>>>> siena subject_predrug.nii.gz subject_postdrug.nii.gz
>>>> siena subject_preplacebo.nii.gz subject_postplacebo.nii.gz
>>>
>>> As suggested on the website I then did >run siena_flow2std A B< and
>>> used fslmerge to merge all the A_to_B_flow_to_std.nii.gz into one 4D
>>> file (all_flow_to_std.nii.gz) so that first all the 20 were flow
>>> images between Pre and Post for the DrugCondition and the last 20
>>> were the changes under the Placebo Condition. I then set up matrix
>>> and contrasts with the Glm_gui wizard to set up a paired ttest and
>>> used randomise with the threshold-free-enhancement-option.
>>>
>>> As the whole procedure was rather to control that there wasn't any
>>> particular atrophy so I didn't expect any significant results.
>>> However I do get signifant voxels for the Contrast 'Condition B >
>>> Condition A' Contrast and was wondering how to interpret these
>>> findings, would it mean that the atrophy is bigger in the Placebo
>>> Condition?
>>>
>>> Below my design matrix and contrast (example for 5 subjects)
>>>
>>> Input Group EV1 EV2 EV3 EV4 EV5 EV6
>>> 1 1 1 1 0 0 0 0
>>> 2 1 1 0 1 0 0 0
>>> 3 1 1 0 0 1 0 0
>>> 4 1 1 0 0 0 1 0
>>> 5 1 1 0 0 0 0 1
>>> 6 1 -1 1 0 0 0 0
>>> 7 1 -1 0 1 0 0 0
>>> 8 1 -1 0 0 1 0 0
>>> 9 1 -1 0 0 0 1 0
>>> 10 1 -1 0 0 0 0 1
>>>
>>> Contrasts
>>> EV1 EV2 EV3 EV4 EV5 EV6
>>> Condition A>B 1 0 0 0 0 0
>>> Condition B>A -1 0 0 0 0 0
>>>
>>>
>>> Thanks, Michael
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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