Hi,
Reasonable question - however, I still believe that this is fine: the
higher-level .lcon has already (at the start of the higher-level FEAT
run) been created to contain the average of all the relevant first-
level contrasts' PPheight values - this averaging has already been
done and Featquery just reads this single value in.
Hope this answers the query?
Cheers.
On 29 Jan 2008, at 02:00, Stephane Jacobs wrote:
> Hi Steve,
>
> Steve Smith wrote:
>>> 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.
>>
> I'm probably missing something here. I did not check into details for
> FEAT, but I have looked into the Featquery script, and here is what I
> understood: when calculating the scaling factor, it determines whether
> it's a first or higher level analysis just by looking whether a
> design.lcon file exists within the feat directory. If not (first
> level),
> it uses the ppheight from the design.con file, which specifies a
> ppheight value for each EV. If it does find design.lcon (higher
> level),
> however, then it uses the single value contained in this file to scale
> all the copes contained in the feat directory - which, in my case,
> come
> from different 1st level copes. If this is right, then I don't see how
> this ppheight is related only to the relevant 1st level contrasts...
>
> Could you tell me where I'm getting lost here?
>
> Thanks again
>
> Best
>
> Stephane
>
>
>>
>>> 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
>>>> ---------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>>
>> 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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