Hi - please see the GLM intro in the FEAT manual - hopefully this  
should answer things.  In the single EV case, with a [1] contrast, the  
COPE is identical to the PE.
Cheers.



On 25 Feb 2009, at 11:47, Daniel Shaw wrote:

> Liam,
>
> Thanks for your prompt response - it is very much appreciated. It  
> seems I posted my initial question confusingly, however.
>
> I am trying to extract % signal change though Featquery for my  
> higher-level group analysis. For the hands-baseline contrast at the  
> individual lower-level, I did not model the baseline condition - I  
> only modeled one 'hand' EV. However, when I Featquery the results of  
> the group analysis for hands, I can choose from the stats/pe or  
> stats/cope files from the higher-level analysis output. My questions  
> are:
>
> (a) Why should there be a COPE file for this contrast when only one  
> EV (i.e. hands) was modelled? Shouldn't this produce only a PE?
> (b) If the COPE file is derived from the hands PE-baseline PE  
> contrast (with the baseline condition implicitly modelled by FSL),  
> why am I given the option to convert the PE values to a % signal  
> change? Surely only the COPE file will provide a meaningful % signal  
> change, with the PE rendered unnecessary in this case?
>
> I hope this is clearer.
>
> Dan.
>
>
> On Feb 24, 2009, at 5:42 PM, Nestor, Liam (Contractor) wrote:
>
>> Hello Dan
>>
>> What is your baseline? While I ask this question, I am not too sure  
>> you would actually want to want to model it, anyway.  By treating  
>> the baseline as an implicit measure, while specifically modelling  
>> HANDS (the EV in your case), FSL Feat understands that everything  
>> else is the baseline.
>>
>> FSL Feat generally doesn't work with % change scores, but as you  
>> remarked, PEs. So, you should do a lower level analysis on each run  
>> of you task using Feat; then combine the runs using a fixed effects  
>> analysis; then finally input the cope images for the hands EV from  
>> this second level analysis for each subject into a higher level  
>> (e.g., FLAME) to see where your subjects are activating on average  
>> above baseline.
>>
>> The results will be generated as a thresholded zstsat file, which  
>> will consist of different clusters of voxels; the co-ordinates of  
>> which should be generated in the stats report.
>>
>> Liam.
>>
>>
>>
>>
>>
>>
>>
>>
>> *******************************************
>> Liam Nestor, Ph.D
>> Office C8-523
>> Laboratory for Molecular Neuroimaging
>> Semel Institute for Neuroscience and Human Behavior
>> 760 Westwood Plaza
>> Los Angeles 90024
>> Tel: 310-206-0655
>> E-mail: [log in to unmask]
>> *******************************************
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf  
>> Of Daniel Shaw [[log in to unmask]]
>> Sent: Tuesday, February 24, 2009 8:00 AM
>> To: [log in to unmask]
>> Subject: [FSL] Featquery - COPE v PE
>>
>> Hi,
>>
>> I'm desperately trying to decide whether I should convert the stats/ 
>> pe or stats/cope to %
>> signal change for a low-level group analysis (i.e. viewing hands  
>> versus baseline), both of
>> which give different % signal change values.
>>
>> Firstly, since only one EV is explicitly modelled in this case  
>> (i.e. hands) shouldn't there be
>> only one parameter estimate and no COPE? Alternatively, if the  
>> baseline is implicitly
>> modelled and the COPE is the contrast between the two resulting PEs  
>> (i.e hands vs
>> baseline), shouldn't the stats/pe and stats/cope give the same %  
>> signal change values, and
>> why would you be given the option to convert the stats/pe into a %  
>> signal change?
>>
>> I'm really confused, so any help would be greatly appreciated.
>>
>> Dan.
>>
>> IMPORTANT WARNING:  This email (and any attachments) is only  
>> intended for the use of the person or entity to which it is  
>> addressed, and may contain information that is privileged and  
>> confidential.  You, the recipient, are obligated to maintain it in  
>> a safe, secure and confidential manner.  Unauthorized redisclosure  
>> or failure to maintain confidentiality may subject you to federal  
>> and state penalties. If you are not the intended recipient, please  
>> immediately notify us by return email, and delete this message from  
>> your computer.
>
> Daniel Shaw M.Sc.
> PhD student
> Brain & Body Centre
> University of Nottingham
> University Park
> Nottingham
> NG7 2RD
>
>
>
>
> This message has been checked for viruses but the contents of an  
> attachment may still contain software viruses, which could damage  
> your computer system: you are advised to perform your own checks.  
> Email communications with the University of Nottingham may be  
> monitored as permitted by UK legislation.
>


---------------------------------------------------------------------------
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
---------------------------------------------------------------------------