No rule that I know of other than simpler is easier.
The only other thing to check is that you have the latest updates.
Darren
On Aug 5, 2008, at 10:27 AM, "Nugent, Allison C. (NIH/NIMH) [E]" <[log in to unmask]
> wrote:
> My nc is 2, so I have n1+n2+2+2+4 columns.
>
> Is there a rule of thumb for which effects to include?
>
> If I really only need the subject and interaction effects (a n1+n2+4
> column matrix) wouldn't the main effect of group contrast just be
>
> ones(1,n1)/n1 -ones(1,n2)/n2 ones(1,nc)/nc -ones(1,nc)/nc
>
> In any case, I'm at a complete loss as to why these contrasts aren't
> valid for me. I was also working on a much simpler 2 group/no
> conditions spm2 model yesterday, where the design matrix is all the
> subject effects followed by the covariate and the simple [ones(1,n1)/
> n1 -ones(1,n2)/n2] contrast wouldn't work.
>
> Thanks for your help, though - when I execute the commands below, I
> get essentially the same thing.
>
> Allison
>
>
> -----Original Message-----
> From: Darren Gitelman [mailto:[log in to unmask]]
> Sent: Mon 8/4/2008 11:13 PM
> To: Nugent, Allison C. (NIH/NIMH) [E]; [log in to unmask]
> Subject: RE: [SPM] correctly specifying repeated measures mixed
> model in SPM5
>
> Allison:
>
> Your contrast looks correct. I have a set of test analyses and using a
> contrast exactly as you describe below is perfectly valid. By the
> way I
> assume you have n1+n2+2+3+6 columns in your design.
>
> In any case inclusion of the main effects makes the design overly
> complex
> and you can get similar results by only including the subject and
> interaction effects. In that case your group contrast would be
>
> ones(1,n1)/n1 -ones(1,n2)/n2 MEg zeros(1,nc) ones(1,nc)/nc -
> ones(1,nc)/nc
>
> With respect to the roundoff errors, my guess is that this is to be
> expected, although I know nothing about the algorithms for floating
> point
> calculations. Attached is a plot of the rounding errors for every
> combination of n1 and n2 from 1:100.
>
> for n1 = 1:100
> for n2 = 1:100
> out(n1,n2)=sum([[ones(1,n1)/n1], [-ones(1,n2)/n2]]);
> end
> end
> figure
> surf(1:100,1:100,out)
> shading interp
>
> It makes a very pretty picture, and as you can see there is some
> type of
> systematic variation in the roundoff errors that gradually increases
> as n1
> and n2 increase. I don't know if this is related to floating point
> calculations at the machine level or from matlab. The numbers vary
> between
> -4.16e-015 to 4.13e-015. There are some actual zeros in the
> calulation, but
> they don't have any obvious pattern. See the black and white figure.
> Nevertheless, I don't think this is what is giving you the problem
> though as
> the contrast works as noted above.
>
> sorry not to be of more help.
> darren
>
>> -----Original Message-----
>> From: Nugent, Allison C. (NIH/NIMH) [E] [mailto:[log in to unmask]]
>> Sent: Tuesday, August 05, 2008 8:45 AM
>> To: Darren Gitelman; [log in to unmask]
>> Subject: RE: [SPM] correctly specifying repeated measures
>> mixed model in SPM5
>>
>> It's still not working - I split this original post into two threads.
>>
>> I was originally trying to evaluate the full "main effect of
>> group" contrast from page 10 of Jan's tutorial.
>>
>> Briefly, n1 and n2 are the N for groups 1 and 2 nc=num of
>> conditions=2, ng=number of groups=2
>> MEg=[1 -1]
>>
>> For a design matrix containing (in this order) subject
>> effects, groups effects, condition effects, and
>> group*condition interaction effects, the main effect of gruop
>> contrast is:
>>
>> ones(1,n1)/n1 -ones(1,n2)/n2 MEg zeros(1,nc) ones(1,nc)/nc
>> -ones(1,nc)/nc
>>
>> At one point I got this to work, but I only seem able to
>> replicate failure and not success.
>>
>> I've tried just the first portion: ones(1,n1)/n1
>> -ones(1,n2)/n2, which should be a valid contrast on its own,
>> but I still get the "invalid contrast" message. And, when I
>> sum the contrast in the matlab window, its close, but not
>> equal to zero.
>>
>> In fact, even this:
>>
>> sum([ones(1,10)/10 -ones(1,4)/4])
>>
>> which should be evaluated to 0 without any problem with
>> rounding erroris evauated as:
>>
>> -1.1102E-16
>>
>> Which makes me believe that something is seriously wrong with
>> my matlab configuration. Has anyone seen this before?
>>
>> Allison
>>
>> -----Original Message-----
>> From: Darren Gitelman [mailto:[log in to unmask]]
>> Sent: Mon 8/4/2008 4:30 AM
>> To: Nugent, Allison C. (NIH/NIMH) [E]; [log in to unmask]
>> Subject: RE: [SPM] correctly specifying repeated measures
>> mixed model in SPM5
>>
>> Allison
>>
>> This should work. It is close to eps (minimum number in
>> Matlab). What contrast are you trying to set up and what is
>> your design?
>>
>> Darren
>>
>>> -----Original Message-----
>>> From: SPM (Statistical Parametric Mapping)
>> [mailto:[log in to unmask]]
>>> On Behalf Of Allison Nugent
>>> Sent: Monday, August 04, 2008 2:08 PM
>>> To: [log in to unmask]
>>> Subject: Re: [SPM] correctly specifying repeated measures
>> mixed model
>>> in SPM5
>>>
>>> I think I spoke too soon regarding my success with getting symbolic
>>> contrasts to work. At one point, I did manage to make this
>> work, but
>>> now,
>>>
>>> sum(ones(1,n1)/n1 -ones(1,n2)/n2)) = 9.43E-16
>>>
>>> instead of zero, which is exasperating! Is there something I can
>>> change in my setup to fix this?
>>>
>>> Thanks!
>>>
>>> Allison
>>>
>>
>>
>>
>
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