thank you, Cornelius
it helps a lot
> On Fri, Apr 1, 2011 at 11:28 AM, Angela Favaro <[log in to unmask]>
> wrote:
>> Hi Cornelius,
>> thank you for your reply.
>> However, you did not completely answer to my doubts.
>> Let me make an example:
>>
>> I am studying a brain area whose connectivity (resting state) seems to
>> show a positive correlation with a cognitive variable in the patient
>> group
>> and a negative correlation with the same variable in the control group.
>> This cognitive variable also differ between groups.
>> If I want to test the differences between groups in SLOPES, I will
>> demean
>> within groups. Is it right?
>
> If the intercept is of no interest and you are sure not to affect your
> contrasts of the mean regressors in an invalid way, I'd say yes.
>
>> If I want to test the differences between groups in connectivity
>> removing
>> the effects of the cognitive variable (suppose this has some sense), I
>> will demean across groups or (according to type of variable) I can not
>> demean at all. Right?
>
> Again, I'd say yes.
>
>> For the second question: in a design with two groups and a covariate of
>> interest demeaned across groups. Do I need to use the -D option? And
>> what
>> if the demeaning is within groups?
>
> If you have regressors modelling the mean (say, one regressor with 1's
> for each patient and 0's for controls, and a second regressor with the
> other way around), you should not need the -D option. If there is no
> mean regressor but only one regressor demeaned across groups, you
> probably need the -D flag, as far as I got it. If you demeaned within
> groups in this setting, you probably also need the -D flag, but you
> will be testing for slopes only - any difference of the mean will not
> appear in your test statistics. If the lines were parallel in that
> setting, but miles apart, you wouldn't see it.
> Before taking this all for true, I'd advise also checking on all the
> previous posts in other threads - might be I missed something myself.
>
> Hope that helps,
> Cornelius
>
>> Thanks!
>> Angela
>>
>>
>>> Hi Angela,
>>>
>>> let's see if I got it right.
>>>
>>> 1) Besides testing for slopes, I am also interested in average group
>>> differences. Thus, if ages weren't matched, I would be introducing a
>>> confound, i.e., any effect introduced by progressing age (e.g. task
>>> speed) would also influence the group mean. As long as I demean ACROSS
>>> groups, this will not influence the *group means* and their contrasts
>>> - in the GLM, any *shared* variability simply disappears (and will
>>> lower "sensitivity" of either contrast, and rightly so. Teaches me to
>>> match groups the next time, as Jesper put it two days ago).
>>> If, on the other hand, I demeaned only within groups, I would not
>>> correct for the fact that there was a significant contribution of the
>>> factor "age" to either group. All variability due to the difference of
>>> age means would be soaked up by the group means and their contrasts.
>>> Therefore, if these group contrasts showed something significant, it
>>> might have been just due to the age difference (group a is slower than
>>> b, but also happens to be the older one!), but not due to treatment or
>>> diagnosis, or whatever I was actually interested in.
>>>
>>> 2) As far as I got it, if you are only interested in correlations with
>>> a (demeaned) covariate and did not model any group mean, you also
>>> should demean the data before "randomise"ing. As an example: running
>>> randomise on VBM data of a depressed patient cohort, looking for GM
>>> changes correlating with a suicidal ideation score ranging from -5 to
>>> +5, mean 0. In this case, randomise -D will do the demeaning of the
>>> DATA (not the covariates) for you, saving you the effort of running
>>> fslmaths on the data.
>>>
>>> If anything of this is wrong, I am sure one of the other contributors
>>> will point it out rather quickly and I'll have lost posting rights for
>>> 4 weeks or so :-)
>>>
>>> Cheers,
>>> Cornelius
>>>
>>> On Thu, Mar 31, 2011 at 11:36 PM, Angela Favaro
>>> <[log in to unmask]>
>>> wrote:
>>>> Dear FSL Masters,
>>>> this discussion has been very helpful for me.
>>>> But I still have two doubts:
>>>> 1. Demeaning within groups is more an exception than a rule, but it is
>>>> the
>>>> correct thing when I want to test differences between slopes (and not
>>>> differences between groups). Is it correct?
>>>> In the example below the two groups have a similar age. What happens
>>>> if
>>>> the covariate differs in the two groups?
>>>>
>>>> 2. What continues to be unclear to me is the use of the -D option in
>>>> randomise. When is it necessary/advisable to use it? Only in one group
>>>> covariate analysis?
>>>>
>>>> Thank you
>>>>
>>>> Angela
>>>>
>>>>
>>>>
>>>>> Yeah, that's what I thought. And basically that's why I asked in the
>>>>> first place :-)
>>>>> But thanks for all the contributions to this topic. I believe I have
>>>>> an idea on how to go about it, now.
>>>>> Best regards,
>>>>> Cornelius
>>>>>
>>>>> On Thu, Mar 31, 2011 at 5:06 PM, Michael Harms
>>>>> <[log in to unmask]>
>>>>> wrote:
>>>>>> Just wanted to chime in that demeaning the performance EV separately
>>>>>> within group is a rather unique case that is specific to this
>>>>>> particular
>>>>>> post.
>>>>>>
>>>>>> Recent posts by Jesper (just yesterday), Jeannette, Tom, and myself
>>>>>> have
>>>>>> all advised that, in general, one should demean across all subjects
>>>>>> (NOT
>>>>>> within group separately).
>>>>>>
>>>>>> Given the recent posts on this, I thought it was worth making
>>>>>> explicit
>>>>>> that demeaning within groups is not a "typical" situation.
>>>>>>
>>>>>> And as a matter of good reporting practice, any time that demeaning
>>>>>> is
>>>>>> performed separately within group, rather than across all subjects,
>>>>>> that
>>>>>> should be noted (and justified) very explicitly in any presentation
>>>>>> of
>>>>>> the ensuing results.
>>>>>>
>>>>>> cheers,
>>>>>> -MH
>>>>>>
>>>>>> On Thu, 2011-03-31 at 08:42 +0100, Stephen Smith wrote:
>>>>>>> Hi
>>>>>>>
>>>>>>> On 30 Mar 2011, at 11:30, Cornelius Werner wrote:
>>>>>>>
>>>>>>> > Hi,
>>>>>>> >
>>>>>>> > sorry to revive such a well-worn topic. But there is something I
>>>>>>> did
>>>>>>> > not quite get so far.
>>>>>>> > As an example, I am examining a patient cohort and a control
>>>>>>> cohort
>>>>>>> > in
>>>>>>> > a Dual Regression setup (resting state data). Patients and
>>>>>>> controls
>>>>>>> > are matched for age and gender. They obviously differ in
>>>>>>> diagnosis,
>>>>>>> > but also in one performance score. I am interested in basic group
>>>>>>> > differences and the differential correlation of connectivity
>>>>>>> > strength
>>>>>>> > of several RSNs with performance. For the final randomise-step,
>>>>>>> my
>>>>>>> > design matrix has a column for group mean "patient" and one for
>>>>>>> > "controls" (consisting of 1, padded with zeroes where
>>>>>>> applicable),
>>>>>>> > and
>>>>>>> > two separate columns for age (as a confounder) - one for each
>>>>>>> group,
>>>>>>> > respectively, because an age*group interaction on connectivities
>>>>>>> > could
>>>>>>> > not be excluded a priori. As I was modelling the group mean
>>>>>>> > separately, only the slopes associated with age were tested. Is
>>>>>>> that
>>>>>>> > correct so far?
>>>>>>>
>>>>>>>
>>>>>>> I think so - sounds fine.
>>>>>>>
>>>>>>> > As the age means did not differ (tested beforehand),
>>>>>>> > does it matter if I demeaned within group or across groups?
>>>>>>> > Shouldn't
>>>>>>> > the intercept be modelled by the group mean regressor, in any
>>>>>>> case?
>>>>>>> > Following Tom's last post, I'd probably demean across groups.
>>>>>>> >
>>>>>>> > The next thing is even more unclear to me:
>>>>>>> > Due to an expected group*performance interaction (i.e. steeper
>>>>>>> slope
>>>>>>> > of increases in connectivity along with better performance in
>>>>>>> > contrast
>>>>>>> > to the other group), also the performance scores are split. BUT:
>>>>>>> > should I demean?
>>>>>>>
>>>>>>>
>>>>>>> Yes - if you want to compare the *slopes* between the two groups,
>>>>>>> demean the performance scores within group before padding with
>>>>>>> zeros,
>>>>>>> for each group's performance EV.
>>>>>>>
>>>>>>> > And if so, within groups, or across groups? In this
>>>>>>> > case, mean differences in performance are believed to be *due to*
>>>>>>> > diagnosis - therefore, variability associated with the mean
>>>>>>> should
>>>>>>> > go
>>>>>>> > to the group regressor, shouldn't it? In this case, I'd be
>>>>>>> inclined
>>>>>>> > to
>>>>>>> > demean in order not to affect the group mean regressor
>>>>>>> negatively,
>>>>>>> > and
>>>>>>> > to demean within groups, because of the (clearly) attributable
>>>>>>> mean
>>>>>>> > variability...?!
>>>>>>> >
>>>>>>> > Example:
>>>>>>> >
>>>>>>> > EV1: Patient mean
>>>>>>> > EV2: Control mean
>>>>>>> > EV3: Patient age (demeaned across groups - EV of no interest)
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>> I presume you mean demeaned within group, then padded with zeros.
>>>>>>>
>>>>>>>
>>>>>>> Cheers.
>>>>>>>
>>>>>>> > EV4: Control age ( " )
>>>>>>> > EV5: Patient performance score (demeaned within patients)
>>>>>>> > EV6: Control performance score (demeaned within controls)
>>>>>>> >
>>>>>>> > Patients>controls: 1 -1 0 0 0 0
>>>>>>> > Controls>patients: -1 1 0 0 0 0
>>>>>>> > Slope(performance score) patients > Slope(performance score)
>>>>>>> > controls:
>>>>>>> > 0 0 0 0 1 -1
>>>>>>> > Slope(performance score) controls > Slope(performance score)
>>>>>>> > patients:
>>>>>>> > 0 0 0 0 -1 1
>>>>>>> >
>>>>>>> > Please don't hit me - I'm having a hard time getting my head
>>>>>>> around
>>>>>>> > this :-)
>>>>>>> > Cheers,
>>>>>>> > Cornelius
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>> ---------------------------------------------------------------------------
>>>>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>>>>> Associate Director, Oxford University FMRIB Centre
>>>>>>>
>>>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>>>>> +44 (0) 1865 222726 (fax 222717)
>>>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>>>>> ---------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Dr. med. Cornelius J. Werner
>>>>> Department of Neurology
>>>>> RWTH Aachen University
>>>>> Pauwelsstr. 30
>>>>> 52074 Aachen
>>>>> Germany
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Dr. med. Cornelius J. Werner
>>> Department of Neurology
>>> RWTH Aachen University
>>> Pauwelsstr. 30
>>> 52074 Aachen
>>> Germany
>>>
>>>
>>
>
>
>
> --
> Dr. med. Cornelius J. Werner
> Department of Neurology
> RWTH Aachen University
> Pauwelsstr. 30
> 52074 Aachen
> Germany
>
>
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