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
> ---------------------------------------------------------------------------
>
>
>
|