Dear Darren,
d gitelman wrote:
> Hi Matt/Will/SPM
>
> I've been reading over this thread. I have a couple questions and I also run
> into trouble specifying appropriate contrasts.
>
> My experiment has 21 subjects in 2 groups- 9 in group 1, and 12 in group 2.
> Each subject performs 3 levels of a task which is an n-back working memory
> task.
>
> Following the discussion I should have 3 factors (i think)
> Independence Variance
> Subject Yes Equal?
> Group Yes Unequal
> Condition No* Unequal
>
> I would think that condition should be non-independent because they all are
> drawn from the same subject, but in Will's original email on this topic he
> chose independent, which I don't understand.
>
> Would the variance setup be correct?
>
> ------
> I then chose 1 main effect of subject and 1 interaction of factors 2 and 3.
>
> this produces a design matrix (attached) with 21 subject columns, then 3
> columns of the interaction of group 1 with each condition and 3 columns with
> the interaction of group 2 with each condition.
> ------
>
> I can examine some t-tests on the interaction columns. For example this
> contrast is valid (looking at group differences of condition differences)
> zeros(1,21) 1 0 -1 -1 0 1
>
> but this contrast is not valid (looking at group differences of single
> conditions)
> zeros(1,21) 1 0 0 -1 0 0
>
If you think about this contrast in the following way I hope you can see
why it is invalid. Consider first, just the part of your design matrix
for the first 9 subjects (ie. the first group). This contains the 9
subject effects and the 3 condition effects. Now, if you try doing
a [1 0 0] contrast here, this will be invalid; we can only use contrasts
that look for differences among the conditions (you know this from your
later reply to Matt :-)). The same consideration goes for the second
part of the design matrix; you can't do a [-1 0 0]. Therefore its not
surprising you can't do [1 0 0 -1 0 0] for the whole design matrix.
This logic also means you can't test for eg. a main effect of group !!
Which is of course a main reason for setting up the design in the first
place.
So, my advice is as follows. Don't use designs that mix (i)
within-subject effects (ie. condition) with (ii) between subject effects
(group).
Within-subject designs with just 1 factor (eg. 'condition') are fine.
You can test for between group differences in working memory as follows.
Take two levels of working memory eg. condition 3 minus condition 1.
Make this contrast for each subject at the first level. Then use these
differential contrasts in a two sample t-test at the second level (where
the two samples are the two groups).
Am cc'ing Karl on this one as I don't want to mislead anyone.
Happy New Year,
Will.
PS. 'repl' is now obsolete.
> ------
> For the main effect of condition I did an F test
> [ zeros(1,21) 1 -1 0 1 -1 0
> zeros(1,21) 0 1 -1 0 1 -1]
>
> Is this correct? It seems to be valid.
>
> ------
>
> I cannot seem to specify a valid contrast for the main effect of group.
>
> t-test: ones(1,9) -1*ones(1,12) <- invalid
> f-test: ones(1,9) -1*ones(1,12) <- invalid
> f-test: zeros(1,21) 1 1 1 -1 -1 -1 <- invalid
>
> and also invalid is the following.
> f-test: zeros(1,21) 1 0 0 -1 0 0
> zeros(1,21) 0 1 0 0 -1 0
> zeros(1,21) 0 0 1 0 0 -1
>
> any suggestions or comments? I have attached the design matrix.
>
> Darren
>
> ----------
> Darren Gitelman, MD
> Department of Neurology
> Northwestern University
> voice: (312) 908-8614
> fax: (312) 908-5073
> page: (312) 695-1849
> email: [log in to unmask]
> ----------
>
>> -----Original Message-----
>> From: SPM (Statistical Parametric Mapping)
>> [mailto:[log in to unmask]] On Behalf Of Matt Shane
>> Sent: Thursday, December 20, 2007 2:44 PM
>> To: [log in to unmask]
>> Subject: Re: [SPM] questions on perfroming 2 x 2
>> within-subjects ANOVA in SPM5
>>
>> Dear Will (or anyone else who can help),
>>
>> Your reply to Michiru was very timely for me, and I have just
>> attempted to undertake an analysis guided by your steps
>> below. I feel like the design matrix is correct, but
>> unfortunately the contrast manager doesn't appear to be
>> appreciating the design I've created. And so I'm thinking
>> that I might have gone astray from your advice in some manner.
>>
>> In short: I have 30 participants in a 3 (Group) x 3
>> (TrialType) mixed-model design. I've thus created 3 factors
>> in the flexible-factorial model: Subject, Group and
>> TrialType. The design matrix (which I'm attaching to this
>> post) appears (to me) to be right: I have 30 subject columns,
>> followed by the three group columns, followed by the three
>> trial-type columns, and finally the group x trial type interactions.
>>
>> My problem arises when I try to create contrasts in the
>> contrast manager, however: I'm able to create contrasts with
>> the first 30 'subject' columns, but I'm told that any
>> contrast utilizing the 'group' or 'trial type' columns is
>> invalid. Which, obviously, is problematic since it's the
>> group and trial type that I want to interrogate!
>>
>> Does anyone have any advice? Have I set up my matrix
>> incorrectly? I'm attaching both the matrix and the .mat file,
>> and would be ever thankful for anyone willing to take the
>> time to look it over.
>>
>> Thanks,
>> Matt
>>
>> __________________________
>> Matthew S. Shane, Ph.D.
>> Research Scientist
>> The MIND Institute
>> 1101 Yale Blvd NE
>> Albuquerque, NM, 87131
>> (505) 272-4374
>> [log in to unmask]
>>
>>
>>
>> -----Original Message-----
>> From: SPM (Statistical Parametric Mapping) on behalf of Will Penny
>> Sent: Thu 12/20/2007 9:20 AM
>> To: [log in to unmask]
>> Subject: Re: [SPM] questions on perfroming 2 x 2
>> within-subjects ANOVA in SPM5
>>
>> Dear Michiru,
>>
>> This is most easily done using the 'Flexible Factorial'
>> option.
>>
>> 1. Create two factors.
>>
>> 2. Call the the first one Subject. Independence Yes, Variance Equal.
>>
>> 3. Call the second one 'Condition'. Independence Yes,
>> Variance Unequal.
>>
>> 4. Under, Specify Subjects or all Scans, Choose Subjects
>>
>> 5. Under Subjects, create a new 'Subject' for each subject
>> that you have eg. 5.
>>
>> 6. Then, for each Subject, under 'Scans'. Enter the 4 scans
>> you have for each subject.
>>
>> 7. Also, for each Subject, under 'Conditions' enter the vector [1:4]
>>
>> 8. Under Main effects and Interactions create 2 main effects;
>> factor 1 and factor 2.
>>
>> 9. Specify other covariates as necessary and your o/p directory.
>>
>> 10. Then save your design job as 'within_subject_design' and
>> press run.
>>
>> I have attached my saved job file 'within_subject_design.mat'
>> as a template for you. When you run it, SPM should create the
>> design matrix shown in 'design-matrix.png'.
>>
>> Note the 5 subject columns on the left. Without these 5
>> columns you do not have a 'within-subject' design.
>>
>> Also I have treated your 2 x 2 design as a 1 x 4. So you'll
>> need to bear this in mind when doing your contrasts eg. 1 1
>> -1 -1 and 1 -1 1 -1 to test for main effects and 1 -1 -1 1
>> for the interaction (of course, pre-pad these with 5 0's).
>>
>> Best wishes,
>>
>> Will.
>> Michiru Makuuchi wrote:
>>> Hi,
>>>
>>>
>>> I have tired to perfrom 2 x 2 within-subjects ANOVA in SPM5, but I
>>> couldn't find how I could do that in 'Full factorial'
>> dsign. Therefore
>>> I designed the design matrix via 'Multiple regression' option. The
>>> resulted design matrix was similar to Fig 7 of Henson and Penny's
>>> online document (ANOVA and SPM). The difference was only
>> the position
>>> of constant term. In Fig 7, it was the 4th column, but it
>> was on the
>>> last column in my design matirix.
>>>
>>> Here are my questions.
>>> Is my approach acceptible for the purpose?
>>> Can someone point out the exact procedure to build the
>> model for 2 x 2
>>> within-subject ANOVA?
>>>
>>>
>>> Best regards,
>>>
>>> Michiru
>>>
>>> Michiru Makuuchi
>>> Max Planck Institute
>>> for Human Cognitive and Brain Sciences Stephanstrasse 1a, 04103
>>> Leipzig, Germany
>>>
>>>
>> --
>> William D. Penny
>> Wellcome Trust Centre for Neuroimaging
>> University College London
>> 12 Queen Square
>> London WC1N 3BG
>>
>> Tel: 020 7833 7475
>> FAX: 020 7813 1420
>> Email: [log in to unmask]
>> URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
--
William D. Penny
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
Tel: 020 7833 7475
FAX: 020 7813 1420
Email: [log in to unmask]
URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
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