Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

2017-10-11 Thread Douglas N Greve 
the rational is to make them sum to 1.0 so that the gamma.mgh file has 
units of mm (or whatever the input units are). It is unimportant for 
p-values.


On 10/10/2017 01:54 PM, std...@virgilio.it wrote:
> Thanks
>
> In which contrast I must change "1" with "0.25"?
> What is the rationale to use 0.25?
>
>
> Sent from Virgilio Mobile
> 
>
> Il 10/10/2017, Douglas N Greve <gr...@nmr.mgh.harvard.edu> ha scritto:
>
> I don't understand what you mean by "where I should use"
>
> I thought I looked through all those contrasts a few weeks ago, no?
>
>
> On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
>> You have suggested to use
>> 0 0 0 0 .25 .25 .25 .25
>> to look the map where, considering the group differences, the covariate
>> predicts the dependent variable (functional connectivity) in 4GV1.
>>
>> Below I'm reporting the contrast that I have used.
>> Please could you check it and suggest correction?
>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>>
>> Thanks
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>> C15) group.effect.intercept
>> 1 -1 0 0 0 0 0 0
>> 1 0 -1 0 0 0 0 0
>> 1 0 0 -1 0 0 0 0
>> C16) group.effect.slope
>>> 0 0 0 0 1 -1 0 0
>>> 0 0 0 0 1 0 -1 0
>>> 0 0 0 0 1 0 0 -1
>>
>>
>>
>>
>>
>>
>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>>> Thank you very much.
>>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>>> Which are the contrast reported below that I should modify?
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>> C15) group.effect.intercept
>>> 1 -1 0 0 0 0 0 0
>>> 1 0 -1 0 0 0 0 0
>>> 1 0 0 -1 0 0 0 0
>>> C16) group.effect.slope
>>> 0 0 0 0 1 -1 0 0
>>> 0 0 0 0 1 0 -1 0
>>> 0 0 0 0 1 0 0 -1
>>> Messaggio originale
>>> Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>> Data: 9-ott-2017 22.56
>>> A: <freesurfer@nmr.mgh.harvard.edu>
>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance
>>>
>>> I don't know what you are asking
>>>
>>>
>>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>>>> Thank you very much.
>>>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>>>> Which are the contrast reported below that I should modify?
>>>>
>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>>> C15) group.effect.intercept
>>>> 1 -1 0 0 0 0 0 0
>>>> 1 0 -1 0 0 0 0 0
>>>> 1 0 0 -1 0 0 0 0
>&g

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

2017-10-10 Thread stdp82 
Thanks

In which contrast I must change "1" with "0.25"?
What is the rationale to use 0.25?


Sent from Virgilio Mobile


Il 10/10/2017, Douglas N Greve <gr...@nmr.mgh.harvard.edu> ha scritto:

I don't understand what you mean by "where I should use"

I thought I looked through all those contrasts a few weeks ago, no?


On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
> You have suggested to use
> 0 0 0 0 .25 .25 .25 .25
> to look the map where, considering the group differences, the covariate
> predicts the dependent variable (functional connectivity) in 4GV1.
>
> Below I'm reporting the contrast that I have used.
> Please could you check it and suggest correction?
> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>
> Thanks
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>
>
>
>
>
>
> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>> Thank you very much.
>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>> Which are the contrast reported below that I should modify?
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>> C15) group.effect.intercept
>> 1 -1 0 0 0 0 0 0
>> 1 0 -1 0 0 0 0 0
>> 1 0 0 -1 0 0 0 0
>> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>> Messaggio originale
>> Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>> Data: 9-ott-2017 22.56
>> A: <freesurfer@nmr.mgh.harvard.edu>
>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance
>>
>> I don't know what you are asking
>>
>>
>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>>> Thank you very much.
>>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>>> Which are the contrast reported below that I should modify?
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>> C15) group.effect.intercept
>>> 1 -1 0 0 0 0 0 0
>>> 1 0 -1 0 0 0 0 0
>>> 1 0 0 -1 0 0 0 0
>>> C16) group.effect.slope
>>> 0 0 0 0 1 -1 0 0
>>> 0 0 0 0 1 0 -1 0
>>> 0 0 0 0 1 0 0 -1
>>>
>>>
>>>> Messaggio originale
>>>> Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>> Data: 3-ott-2017 16.19
>>>> A: <freesurfer@nmr.mgh.harvard.edu>
>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance
>>>>
>>>> probably you want 0 0 0 0 .25 .25 .25 .25
>>>>
>>>>
>>>>
>>>> On 10/3/17 10:10 AM, std...@virgilio.it wrote:
>>>>> Many thank