hi James
as far as parametric modulation goes--you should read this presentation:
www.fil.ion.ucl.ac.uk/spm/doc/mfd/2008/parametric.ppt
However, you don't always need parametric modulation--it's only
relevant when you have reason to believe that responses to your
stimuli will vary as a function of some other measure (classic example
being reaction time). Thus, if you believe that responses will vary
as a function of RT, it behooves you to include these in the analysis
as the variance due to RT will now be modeled and will not be in your
error term, increasing your power to detect effects of interest. If
you were interested in the effect of RT, you could look at this too.
the motion parameters from realignment should be entered with the
multiple regressors selection in the window you sent a picture of if
you want variance associated with them to be modeled--a good idea!
Anyway, the setting up of contrasts is covered in that presentation as
well. best of luck.
JK
On Thu, Feb 11, 2010 at 3:00 PM, Julie E McEntee <[log in to unmask]> wrote:
> Hi James,
>
> Figure I'd take a shot at your questions- in hopes that any error in my response will be corrected by the experts.
>
> First, if your end goal is a regression at what is called the 2nd-level (group comparison)- meaning inquiring whether BOLD is related to an independent variable, like age, for each subject, you would enter the independent variable as a vector (one number/subject) in the covariates section of the multiple regression.
>
> At the 1st-level, where you specify the model for each subject, the parametric modulations section is used to include, for ex., motion regressors from realignment. Here, you have a number for each scan in your fMRI session (maybe 200-300).
>
> The contrast depends on your task/model and question. A simple fMRI may have 2 task conditions (A, B) separated by rest. If you were interested in task A minus task B, and you entered the conditions into the model in the order task A, task B, rest (take a look at the design matrix for order of conditions), then the contrast weights would be:
>
> 1 -1
>
> Specifically, in the contrast manager window, select t-contrasts (see below), Define new contrast..., enter the name for the contrast (doesn't matter- "A-B") in name box, and enter contrast weights (above) in contrast box- click submit- should say contrast valid; click OK. Click on contrast name in contrast manager and Done to continue to results section (here just choose defaults to generate *con file which you will use in 2nd-level analysis).
>
> As regards difference between t and F-tests, wikipedia probably has a good explanation or any beginner stats textbook. Basically, at the 1st-level, majority of the time you be interested in t-test as F-test has no directionality, but there may be circumstances when F-tests are used at 1st-level. At 2nd-level F-tests are used in factorial (analysis of variance/ANOVA), but need to be followed with t-tests to determine which groups differ and/or directionality.
>
> As regards SPM manual, take a look at examples of data analysis for more info.
>
> To do a regression at the 2nd level, within Multiple regression, enter *con files for each subject under Scans and your independent variable (vector with 1 number/subject) under Covariates. You will need to specify contrasts again; a contrast weight of "1" will give you positive relationship between BOLD and covariate; "-1" the opposite.
>
> Hope this is helpful,
>
> Julie
>
> Julie E. McEntee, M.A., C.C.R.P.
> Senior Research Program Coordinator
> Department of Psychiatry- Neuroimaging
> Johns Hopkins University School of Medicine
> 600 N. Wolfe St./ Phipps 300
> Baltimore, MD 21287
> Phone: 410-502-0468
> Fax: 410-614-3676
>
> ----- Original Message -----
> From: James <[log in to unmask]>
> Date: Thursday, February 11, 2010 9:08 am
> Subject: [SPM] SOS (3rd time): How to construct contrast for parametric modulation?
> To: [log in to unmask]
>
>
>> Dear SPMERS,
>> Could you help me with the following questions. I have inquired them
>> twice in
>> this forum but got no response at all. This is the 3rd time; wish to
>> get some
>> response this time.
>> Looking forward to your reply.
>> Thank you very much!
>> James
>>
>> I need to do regression analysis (the independent variables in the
>> regression
>> are independent variables in the experiment design). I heard that it
>> should use
>> the "parametric modulations", as highlighted in the attached picture,
>> right?
>> (pls check the highlight in the attached picture, thanks!)
>>
>> After implementing the parametric analysis, there will be no contrast
>> in the
>> contrast window. how to define the contrast (pls very specially)? in
>> the define
>> contrast window, there are t-test and F-test and we have to choose
>> one -
>> which one to choose and what to do after that?
>>
>> could you also tell me which file(s) on internet (preferably on
>> www.fil.ion.ucl.ac.uk/spm) or which book(s) do address exactly these
>>
>> questions (I cannot find it in SPM8 manual.)
>>
>
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