Hi Steve,
Thanks for your answer. I guess you were talking about the way things
happen when one runs a usual 2nd level analysis, feeding feat
directories into it. I should have made more clear that I was re-posting
a question that did not get an answer a little time ago, sorry. In my
case, I have defined several contrasts vs modeled rests at the first
level, and fed cope images into the 2nd level analysis because I had to
contrast different conditions coming from different runs. Now I want to
get the percent signal change related to the contrasts defined at the
first level. However, my 2nd level analysis has output only one
cope1.feat directory, since it had cope images as inputs. Then, there is
only one design.lcon file, which contains an average ppheight computed
across all 1st level contrasts, right?
My question was: is this correct in this case to go back to the first
level design.con file, and selectively average the ppheight value for
each contrast separately, and have featquery use those instead?
Thanks again for your time!
Stephane
Steve Smith wrote:
> 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
>>>
>>>
>>>
>>
>
>
> ---------------------------------------------------------------------------
>
> 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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