On Thu, Nov 29, 2012 at 4:55 AM, Anja Dietrich <[log in to unmask]> wrote:
> Dear Donald,
>
> thank you very much for the help!
>
> After calculating the contrasts, some new questions came up
> (especially related to OrthoView). Sorry for bothering you again, but
> hope you can help.
>
> 1. Why you set "I.Cons(x).Levs=2" to "2"?
Because in your comparison there were two levels G1C1 and G1C2.
>
> 2. Is it possiple to display the number of voxels of a cluster in OrthoView?
Not automatically. If you click get peak info, then you will get a
table with cluster sizes, you'll have to download peak_nii toolbox
first though.
>
> 3. Is there an opportunity to plot effect sizes of defined ROIs in
> OrthoView. Up to now I did that by rfxplot, but I find no way to
> realize this with the data of the GLM Flex analysis.
No. However, you can plot the effects. Just click plot sphere, plot
cluster, etc.
Effect size refers to a specific statistical term.
>
> 4. If I tried to find local maxima via right-click and "Go to local
> maxima" always the following error occurs: ??? Undefined function or
> method 'neighbors' for input arguments of
> type 'double'. Error in ==> OrthoView>gotoMinMax at 2298
> neigh = neighbors(currloc,Obj(vn).h.dim);
> What is the problem?
Did you download the Utilities toolbox from the download page? It
should be included in that zip file.
>
> 5. You recommended to take imcalc for calculation of the F-contrasts (T^2).
> I tried this: took 1 of the T-maps as input file and set current item
> expression to i^2
> The process failed because an "incompatible image" has been produced.
> Could you see the mistake?
Use i1.^2
>
> 6. Why you set ET to 1 in the following contrast. Isn't it a
> withinn-subject comparison?
> Any condition different than 0:
> I.Cons(x).Groups={columns representing factor 2} [4 5]
> I.Cons(x).Levs=0;
> I.Cons(x).ET=1;
No. This is a between subject contrast as you are asking if either
level of factor 2 is significantly different than 0. If you had asked
C1 is different from C2, then the ET would be 2.
> I.Cons(x).Groups={columns representing factor 2} [4 5]
> I.Cons(x).Levs=2;
> I.Cons(x).ET=2;
Hope this helps.
>
> Thank's a lot in advance!
>
> Anja
>
>
>
> 2012/11/27, MCLAREN, Donald <[log in to unmask]>:
>> The F-contrast is simply T^2 with DF(1,df of T) when then are only 2
>> levels being compared. For simplicity we GLM Flex only reports the T.
>> You could create the F by using imcalc can squaring the T-statistic
>> image.
>>
>> If you use OrthoView to view the results, then you can see the +/-
>> values. When +- values are both shown, the test is treated as
>> two-tailed and will be identical to the F-test.
>>
>> 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 Mon, Nov 26, 2012 at 6:25 PM, MCLAREN, Donald
>> <[log in to unmask]> wrote:
>>> Please see in line responses. Sorry for the delay.
>>>
>>> On Fri, Nov 2, 2012 at 8:59 AM, Anja Dietrich <[log in to unmask]>
>>> wrote:
>>>> Sorry for the empty message. Here is the question:
>>>>
>>>> Dear experts,
>>>>
>>>> since there is no opportunity to compare groups in a flexible factorial
>>>> design in spm, I set up a mixed design ANOVA in GLM flex (see attachment
>>>> for the design matrix).
>>>>
>>>> The model consists of 3 factors:
>>>> group (3 levels)
>>>> condition (2 levels)
>>>> the obligatory subject factor
>>>>
>>>> and a group/ condition interaction
>>>>
>>>> Because contrast definition differs from that in SPM, I would be very
>>>> happy if one can help me to define the contrasts correctly.
>>>>
>>>> First of all I'd like to define a giant f contrast to check if any column
>>>> of the design matrix differs from 0.
>>>
>>>>>>> This doesn't make any sense to do. I presume you want to test if any
>>>>>>> of your group/conditions are different than 0. Here is how to do it.
>>>
>>> Any group different than 0:
>>> I.Cons(x).Groups={columns representing factor 1} [1 2 3]
>>> I.Cons(x).Levs=0;
>>> I.Cons(x).ET=1;
>>>
>>> Any condition different than 0:
>>> I.Cons(x).Groups={columns representing factor 2} [4 5]
>>> I.Cons(x).Levs=0;
>>> I.Cons(x).ET=1;
>>>
>>> Any group/condition pair different than 0:
>>> I.Cons(x).Groups={columns representing the interaction} [6 7 8 9 10 11]
>>> I.Cons(x).Levs=0;
>>> I.Cons(x).ET=1;
>>>
>>>>
>>>> Further I'd like to create F and t contrasts like the following:
>>>> Group1Condition1 / Group2Condition1
>>>
>>> did you mean less than?? Group1Condition1 < Group2Condition1
>>> I.Cons(x).Groups={column for G2C1 then G1C1} [8 6]
>>> I.Cons(x).Levs=2;
>>> I.Cons(x).ET=1;
>>>
>>>> Group1Condition1 > Group2Condition1
>>>
>>> I.Cons(x).Groups={columns for G1C1 then G2C1} [6 8]
>>> I.Cons(x).Levs=2;
>>> I.Cons(x).ET=1;
>>>
>>> ET is 1 for both because these are between-subject comparisons.
>>> [ ] indicates what columns should be in the { }.
>>>
>>>
>>>>
>>>> Thank's a lot in advance!
>>>>
>>>> Anja
>>>>
>>>>
>>>>
>>>
>>> Hope this answers your questions.
>>
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