Thank you Gwenaelle. They were originally 3 groups then we were asked to
do this analysis in 4 groups thats the reason of the confusion. Anyways,
seems like I need to read more to get my head around this.
Cheers
Cagri
2012/1/9 Gwenaëlle DOUAUD <[log in to unmask]>
> Hi Cagri,
>
> your question is clear, but, unless there is indeed a known linear
> relationship between your 3 groups (???), I'm not sure I can make any sense
> of what the reviewer is suggesting (1ev with 1 for controls [sic], 2 for
> group X etc.). Most straightforward thing to do is what Michael Harms has
> suggested in his last post, this should answer (meaningfully) to the
> question of "continuum"...
>
> Cheers,
> Gwenaelle
>
> --------------------------------------------------------------------
> Gwenaëlle Douaud, PhD
> FMRIB Centre, University of Oxford
> John Radcliffe Hospital, Headington OX3 9DU Oxford UK
> Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
> www.fmrib.ox.ac.uk/~douaud
> --------------------------------------------------------------------
> ------------------------------
> *De :* cc yy <[log in to unmask]>
> *À :* [log in to unmask]
> *Envoyé le :* Lundi 9 Janvier 2012 15h15
> *Objet :* Re: [FSL] Re : [FSL] Kernel size (VBM)
>
> Thank you Gwenealle.
>
> Yeah, I will choose the safe way and make sure the reviewer feels
> satisfied :)
>
> I know that you are knowledgable about FSL. I wonder if you have read my
> previous question, which I couldnt find a final answer for. I am copying it
> in case you haven't. I would very much appreciate any contribution. (our
> all discussion is under the topic 'Multiple regression model with a group
> variable (VBM)<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;29cd0501.1201>
> ')
>
> Best
>
> Cagri
>
> Dear FSL experts,
>
> I am reposting this question with the hope of making it more clear this time.
>
> We have 130 subjects in 4 groups (3 patient groups X,Y,Z and a control group) and we compared the GM volumes between these groups in an ANOVA design.
>
> We were asked by a reviewer to do a 'multiple regression with a group variable (e.g. X=4, Y=3, Z=2, Controls=1)' and, 'an independent estimation of group variables' to examine the continuum of GM abnormalities in this sample.
>
> I am copying the exact words of the reviewer to give a better idea about what is asked from us (I just changed the group names):
>
> " the examination of a potential continuum of abnormalities between these groups is likely the more adequate approach. Given the limited statistical power of this study this is probably best examined in the context of a multiple regression model with a group variable (e.g., Group X = 4, Group Y = 3, Group Z = 2, healthy volunteers = 1) and an independent estimation of (potentially unequal) group variances. Given the strong a priori evidence for a continuous increase in gray matter deficits in prefrontal and temporal cortices over groups, one-sided testing of such a model appears legitimate."
>
> How should the design matrix be to test this?
>
> Thank you very much
>
> Cagri Yuksel
>
>
>
>
> 2012/1/9 Gwenaëlle DOUAUD <[log in to unmask]>
>
> Hi Cagri,
>
> alternatively, you can simply do:
>
> fslmaths GM_mod_merg -s 5.1 GM_mod_merg_fwhm12
>
> and then run randomise on GM_mod_merg_fwhm12 ...
>
> A larger kernel size means that you'd pick up differences that are larger
> between your two groups. Unless you had possibly two small peaks that
> merged into a big one by changing the kernel size, if this was not "there"
> at 7mm, there's a good chance it won't "appear" at 12mm, but it's always
> better to please the reviewer and just do it :-)
>
> Cheers,
> Gwenaelle
>
> --------------------------------------------------------------------
> Gwenaëlle Douaud, PhD
> FMRIB Centre, University of Oxford
> John Radcliffe Hospital, Headington OX3 9DU Oxford UK
> Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
> www.fmrib.ox.ac.uk/~douaud <http://www.fmrib.ox.ac.uk/%7Edouaud>
> --------------------------------------------------------------------
> ------------------------------
> *De :* Cagri Yuksel <[log in to unmask]>
> *À :* [log in to unmask]
> *Envoyé le :* Dimanche 8 Janvier 2012 16h34
> *Objet :* Re: [FSL] Kernel size (VBM)
>
> Thank you very much Anderson, just started FSLVBM_3_proc with sigma 5,
> hopefully it'll work.
>
> Well, in our study we compared 3 groups and we couldnt find difference
> between two. The reviewer suggests that the small Kernels are better for
> subcortical structures and larger kernels for cortex (which is actually in
> contrast to what I had read in a recent review paper). So he recommends
> using a larger Kernel to reveal the possible cortical GM differences
> between those 2 groups, which we couldnt find with 7 mm.
>
> Best regards
>
> Cagri
>
> On Sat, 7 Jan 2012 21:18:03 +0000, Anderson Winkler <
> [log in to unmask]> wrote:
>
> >Hi Cagri,
> >
> >This can be changed. Perhaps the easiest is if you open the file
> >${FSLDIR}/bin/fslvbm_3_proc and change the line 103 (for FSL 4.1.9),
> >adding or removing sigmas you want:
> >
> >* for j in 2 3 4 ; do*
> >
> >If you want, for instance, sigmas = 5 and 8 mm, just add:
> >
> >* for j in 2 3 4 5 8 ; do*
> >
> >Then run again the pipeline from this script onwards.
> >
> >I wonder, though, what would be the rationale for the reviewer's
> >request, as we often wish to have less smoothing...
> >
> >Hope it helps!
> >
> >All the best,
> >
> >Anderson
> >
> >
> >
> >On 07/01/12 16:01, Cagri Yuksel wrote:
> >> Dear FSLers,
> >>
> >> We were asked by a reviewer to repeat our VBM study with a FWHM
> kernel size of 12 mm (we reported results in sigma 3mmx2.3=7 mm). However
> as far as I know from the FSL-VBM website the highest kernel size FSL
> allows for VBM analysis is 9 mm (sigma 4x2.3).
> >> Is there a way of doing the VBM analysis with FWHM 12 mm kernel ?
> >>
> >> Thank you,
> >>
> >> Cagri Yuksel
> >>
> >>
> >
> >
>
>
>
>
>
>
