Gabriel
> Dear Cyril
> many thanks and sorry for bodering you again, but in the last I forgot
> to mention that I'm usign a cortical GM mask created by myself, and in
> another study we are using a hippocampus mask, should we use the
> volumes of this masks as the volume regressor instead of the total GM
> volume? and in the latter case should we perform a correction for
> multiple comparisons?
compute the total volume within the mask for each subject and use that
as confounding regressor - and yes you still analyze plenty of voxels
i.e. do plenty of tests therefore you do have to correct for multiple
comparisons
Cyril
>
> I hope that this will be the last question for now.
I hope too ;-)
>
> Thank you
> Gabriel
>
>
>
>
>
>
> > Date: Tue, 15 Dec 2009 11:08:41 +0000
> > From: [log in to unmask]
> > To: [log in to unmask]
> > Subject: Re: [SPM] SPM contrasts
> >
> > Gabriel Go.Es. wrote:
> > > Dear Cyril
> > >
> > > Thank you so much for all your answers,
> > > now I'm perfoming the analysis at once, but should I set the
> > > group just as [1 -1] or [1 0] and [0 -1]?,
> > doesn't matter either [1s and -1s] and a contrast 1 will show gpA > B
> > whereas -1 will show gpB > A or enter 2 columns with [1s 0s] and [0s
> 1s]
> > to model each group and then run the contrasts [1 -1] and [-1 1]
> > > I'm putting all regresors with No centering, is it right?
> > better is to have your data normalized ie centered and of unit variance
> > - if you have your regressor loaded in the workspace simply type
> > zscore(regressor_name)
> >
> > Cyril
> >
> >
> > >
> > >
> > >
> > >
> > >
> > > > Date: Tue, 15 Dec 2009 08:20:25 +0000
> > > > From: [log in to unmask]
> > > > To: [log in to unmask]; [log in to unmask]
> > > > Subject: Re: [SPM] SPM contrasts
> > > >
> > > > Gabriel
> > > >
> > > > your matrix should look a lot like mine in the referenced paper
> - also
> > > > no matter if there is a significant effect of age or not you
> should not
> > > > remove it from the analysis as it will change how data Y are
> projected
> > > > onto X (see SPM book for explanation on the GLM) - linear
> independence
> > > > simply means that no regressor is a combination of the others ;
> this is
> > > > somehow different from correlation and orthogonality ; indeed
> many of
> > > > those combinations are possible (like e.g. correlated and
> independent
> > > > variables), see 'Linearly Independent, Orthogonal, and Uncorrelated
> > > > Variables' by Rodgers et al. The American Statistician
> > > > <http://www.jstor.org/action/showPublication?journalCode=amerstat>,
> > > Vol.
> > > > 38, No. 2, pp. 133-134.
> > > >
> > > > one design matrix should be enough for what you want to do,
> having gp
> > > > (1s and -1s), performance gp A (values and 0s), performances gp
> B, (0s
> > > > and values), age, total GM volume, and scanner as regressors - T
> > > > contrasts [1] and [-1] will test for gp differences, [1 0] and
> [0 1]
> > > for
> > > > performance correlations in each group, [0 1 1] and [0 -1 -1] for
> > > > correlations across groups, [0 1 -1] and [0 -1 1] for differences
> > > > between groups ; all those effects being controlled for age, total
> > > > volume and scanner differences (which exist no matter if
> significant or
> > > > not).
> > > >
> > > > good luck
> > > > Cyril
> > > >
> > > >
> > > > > Dear Cyril,
> > > > >
> > > > > Thank you very much for your quick reply and for the paper
> reference.
> > > > > I have learned a lot of the described statistical approach. I
> would
> > > > > like to confirm that what I'm going to do is correct and at
> the end I
> > > > > will ask you one more question.
> > > > >
> > > > > I will perform within and across-subjects correlations between
> > > > > gray/white matter and performance at the same time that I
> remove the
> > > > > confounding effects of age. In both designs my regressors are
> > > > > performance and age and the contrast should be 0 for scanners,
> 1 for
> > > > > performance (because I expect to find positive correlations),
> and 0
> > > > > for age. I will also compute partial correlations between
> performance
> > > > > and age to ensure lineal independence. If finally they are
> correlated
> > > > > I will remove age from the analysis because I don't have group
> > > > > differences for age.
> > > > >
> > > > > I want also to perform between-subjects correlations to determine
> > > > > whether one group shows higher correlation between GM/WM and
> > > > > performance than the other. Which model and which F-contrast do I
> > > have
> > > > > to use in this case?
> > > > >
> > > > > I’m very sorry to disturb you again. Thank you very much in
> advance
> > > > > for your help.
> > > > >
> > > > > Best regards,
> > > > > Gabriel
> > > > >
> > > > >
> > > > >
> > > > > > Date: Wed, 9 Dec 2009 11:23:52 +0000
> > > > > > From: [log in to unmask]
> > > > > > Subject: Re: [SPM] SPM contrasts
> > > > > > To: [log in to unmask]
> > > > > >
> > > > > > Gabriel
> > > > > > >
> > > > > > > Hello
> > > > > > >
> > > > > > >
> > > > > > > I want to make a correlation between my covariate1 and my
> > > volume loss
> > > > > > > in the scans, without confounding effects of covariate
> 2(age),
> > > what
> > > > > > > contrast should I use: a b or c?
> > > > > > >
> > > > > > >
> > > > > > > age covariate1 scan data
> > > > > > >
> > > > > > > a) 0 -1 0
> > > > > > >
> > > > > > > b) -1 -1 0
> > > > > > >
> > > > > > > c) 1 -1 0
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > and would this be applied for many covariate effects? I mean
> > > to make
> > > > > > > the statistics without confundign the effects of one, 2 or
> three
> > > > > > > covariates, should i set them as you will say to me for
> > > cavariate 2?
> > > > > > >
> > > > > >
> > > > > > the short answer is c = [0 1 0]
> > > > > > the long answer is, assuming one group of subjects, to use a
> > > multiple
> > > > > > regression ion which you enter your covariates with also age,
> > > possibly
> > > > > > age^2, gender, global volume - these last 3 or 4 being the
> 'usual'
> > > > > > confounding factors - using a contrast with 0s everywhere
> except 1
> > > > > or -1
> > > > > > for the covariate of interest will show the voxel correlating or
> > > > > > anti-correlating with you covariate, independently of, or
> > > controlling
> > > > > > for the effect of the other covariates. For more complex
> design with
> > > > > > different groups it's pretty much the same except that you
> can also
> > > > > > contrast covariate - you can find an example of such a
> matrix in the
> > > > > > supplementary material of one of my papers published in HBM 30
> > > > > p2278-2292.
> > > > > >
> > > > > > good luck
> > > > > > cyril
> > > > > >
> > > > > >
> > > > > > --
> > > > > > The University of Edinburgh is a charitable body, registered in
> > > > > > Scotland, with registration number SC005336.
> > > > >
> > > > >
> > >
> ------------------------------------------------------------------------
> > > > > ¡Windows Phone ya está aquí! Mucho más que un teléfono. ¡Hazte con
> > > > > uno! <http://www.windowsphone.com/spain>
> > > >
> > > >
> > > > --
> > > > Dr Cyril Pernet,
> > > > fMRI Lead Researcher SINAPSE
> > > > SFC Brain Imaging Research Center
> > > > Division of Clinical Neurosciences
> > > > University of Edinburgh
> > > > Western General Hospital
> > > > Crewe Road
> > > > Edinburgh
> > > > EH4 2XU
> > > > Scotland, UK
> > > >
> > > > [log in to unmask]
> > > > tel: +44(0)1315373661
> > > > http://www.sbirc.ed.ac.uk/cyril
> > > > http://www.sinapse.ac.uk/
> > > >
> > > >
> > > > The University of Edinburgh is a charitable body, registered in
> > > > Scotland, with registration number SC005336.
> > > >
> > >
> > >
> ------------------------------------------------------------------------
> > > ¡Windows Phone ya está aquí! Mucho más que un teléfono. ¡Hazte con
> > > uno! <http://www.windowsphone.com/spain>
> >
> >
> > --
> > Dr Cyril Pernet,
> > fMRI Lead Researcher SINAPSE
> > SFC Brain Imaging Research Center
> > Division of Clinical Neurosciences
> > University of Edinburgh
> > Western General Hospital
> > Crewe Road
> > Edinburgh
> > EH4 2XU
> > Scotland, UK
> >
> > [log in to unmask]
> > tel: +44(0)1315373661
> > http://www.sbirc.ed.ac.uk/cyril
> > http://www.sinapse.ac.uk/
> >
> >
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> >
>
> ------------------------------------------------------------------------
> Hasta las ovejas de Sietes son expertas en Windows 7. ¡Conócelas!
> <http://www.sietesunpueblodeexpertos.com/>
--
Dr Cyril Pernet,
fMRI Lead Researcher SINAPSE
SFC Brain Imaging Research Center
Division of Clinical Neurosciences
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU
Scotland, UK
[log in to unmask]
tel: +44(0)1315373661
http://www.sbirc.ed.ac.uk/cyril
http://www.sinapse.ac.uk/
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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