Hi,
On 22 Jan 2008, at 16:54, Stephane Jacobs wrote:
> 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?
Sounds right, yes.
> 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?
I think what FEAT/Featquery are doing should be right - it should be
averaging the effective ppheight across all the relevant first-level
contrasts, and as far as I can see this should be correct.
Cheers, Steve.
> 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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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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