Hi,
Yes, this should work fine; FEAT should extract the correct ppheight
values from the correct contrast specification files, according to the
copes that you have selected. It should appropriately estimate the
right average ppheight for each of your second-level contrasts.
Cheers, Steve.
On 15 Jan 2008, at 19:39, Stephane Jacobs wrote:
> Hello,
>
> I had a question about the way the model peak-to-peak height was
> computed for a second level analysis of which input were cope images
> rather than feat directories, and about running featquery on it. I had
> forgotten to mention that I am interested in percent signal change for
> contrasts (condition vs. modeled rest), which explains why I'm looking
> at the ppheight values in design.lcon. Also, I'm looking at contrasts
> that have been set at the first level already, then I have ppheight
> values for each of those and for each first level run.
>
> Can anybody tell me whether I'm doing the right thing here?
>
> Thanks a lot,
>
> Stephane
>
>
> Stephane Jacobs wrote:
>> Hello,
>>
>> I would like to run featquery on a second level analysis (cross
>> session -
>> within subject level) to compute percent change of COPEs within a
>> given ROI.
>> I understand that featquery is using the average ppheight found in
>> the
>> design.lcon file in the copeX.feat directory as a scale factor to
>> compute
>> percent change.
>> However, I am wondering whether this is still correct to do so in
>> my case.
>> Indeed, I have fed cope images into my second level analysis,
>> instead of
>> .feat directories, as I needed to contrast EVs coming from
>> different runs.
>> Then, I end up with one single cope1.feat directory at the output
>> of my
>> second level analysis, which contains as many cope images as I have
>> set
>> contrasts at the 2nd level (4), rather than getting
>> cope1.feat..cope4.feat
>> as when you feed feat directories containing all the same EVs.
>>
>> Therefore, it seems that the value contained in design.lcon is the
>> average
>> of the ppheight across all my contrasts. I wonder if I rather
>> should compute
>> an average ppheight for each of my 2nd level contrast separately,
>> to be more
>> accurate?
>>
>> Thanks in advance for all your thoughts and advice,
>>
>> Best,
>>
>> Stephane
>>
>>
>>
>
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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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