On Wed, Dec 5, 2012 at 9:37 AM, Qasim Bukhari <[log in to unmask]> wrote:
> I m not testing group differences in 1st level, I want to test fixed effect.
> For fixed effect analysis, there is no second level. And I intend to go
> towards second level/random effect, once my fixed effect analysis is true.

>>> I would call this a group fixed analysis to avoid confusion. Calling it a first-level implies subjects AND implies that there would be a second level.

> Regarding null hypothesis, how would I define is then, and where exactly I
> have to define it ?  According to my understanding, null hypothesis is
> defining that there exists no effect; how can I define it in my case then?
> during 'fMRI model specification' ?
> P.S. I m working with resting state data, so there is no 'conditions' that
> are defined.


The null hypothesis is the the connectivity in group 1 equals the
connectivity in group 2.
Ho: G1=G2

Step 1: Make the null hypothesis equal to 0.
Ho: G1-G2=0

Step 2: Convert this to a contrast
1 over the G1 column and -1 over the G2 column, all other columns
should be 0 (if they exist)

==
The F-contrast would be testing that the sum/average of G1 and G2
equals 0. I would expect you would get one brain network appearing
that corresponds to the seed region.

Hope this helps.

>
>
> Qasim Bukhari
>
> Research Assistant and Doctoral Candidate
>
> Institute for Biomedical Engineering
>
> ETH and University Zurich
>
> Wolfgang-Pauli-Strasse 27, HIT E22
>
> webpage: http://www.micro.biol.ethz.ch/people/sybukhar/index
>
>
>
>
>> Date: Wed, 5 Dec 2012 09:20:20 -0500
>> Subject: Re: [SPM] 1st level analysis on F test
>> From: [log in to unmask]
>> To: [log in to unmask]
>> CC: [log in to unmask]
>
>>
>> The null hypothesis is defined before you create the contrasts. The
>> contrasts are based on your null hypothesis.
>>
>> You should not be testing group differences in a 1st level model;
>> rather, you should take estimates of the first level model from each
>> subject to the second level random effects model.
>>
>> Best Regards, Donald McLaren
>> =================
>> D.G. McLaren, Ph.D.
>> Research Fellow, Department of Neurology, Massachusetts General Hospital
>> and
>> Harvard Medical School
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Website: http://www.martinos.org/~mclaren
>> Office: (773) 406-2464
>> =====================
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>>
>> On Wed, Dec 5, 2012 at 9:02 AM, Qasim Bukhari <[log in to unmask]>
>> wrote:
>> > Dear SPM Expert,
>> > I m trying to run an analysis differentiating between the two
>> > population. I
>> > have two groups, group 1 and group 2. These two group differ under one
>> > of
>> > the regressor; which is an extracted time series of region R1. I tried
>> > to
>> > run 3 different experiments
>> >
>> > Experiment 1: group 1 vs group 1 : fixed effect analysis
>> > I input two different subjects but both from group 1. Under the multiple
>> > regressors; I input the extracted time series of region R1. In order to
>> > see
>> > the results; I defined an F-contrast, with (1,1) imagining that its the
>> > same
>> > group so the contrast should also be the same. However in the result; I
>> > see
>> > quite a lot activations. I wasnt expecting that, since these are from
>> > the
>> > same population
>> >
>> > Experiment 2: group 2 vs group 2 : fixed effect analysis
>> > I did the same procedure as described above however this time for group
>> > 2.
>> > The results were same as mentioned above; while I was expecting
>> > contrary.
>> >
>> > Experiment 3: group 1 vs group 2 : fixed effect analysis
>> > This time, I input different subjects from the different groups; however
>> > I
>> > kept the F-contrast as 1, 1. Again I see a lot of activations in the
>> > result,
>> > and I dont have any explanation for this actually
>> >
>> > Experiment 4: group 1 vs group 2 : fixed effect analysis
>> > Same experiment as experiment 3; however I changed the F contrasts to 1,
>> > -1.
>> > Once again I see a lot of activations. Precisely the regressor is region
>> > R1;
>> > which is the acting differently between group 1 and group 2; and while
>> > doing
>> > fixed effect from different population, I would have had expected the
>> > activations in experiment 4. But I m not able to interpret the results
>> > from
>> > other 3 experiments then. Have I understood something wrong ??
>> >
>> > I have another question; when can I define my null hypothesis; can I
>> > define
>> > it before the 2nd level analysis ?? If I understand correctly my null
>> > hypothesis should be defined with the contrast (1,1) ?? is it correct ??
>> >
>> > Thanks a lot
>> > best regards,
>> > Qasim
>> >
>> >
>> >
>> > Qasim Bukhari
>> >
>> > Research Assistant and Doctoral Candidate
>> >
>> > Institute for Biomedical Engineering
>> >
>> > ETH and University Zurich
>> >
>> > Wolfgang-Pauli-Strasse 27, HIT E22
>> >
>> > webpage: http://www.micro.biol.ethz.ch/people/sybukhar/index
>> >
>> >