Hi, back from Hawaii now....catching up....
No - this sounds straightforward so there shouldn't be this inversion.
The randomise-based modelling looks simple and correct - maybe you
should tell us exactly what syntax you used for the randomise command
- and also explain in more detail what you mean by "more direct,
manual, FA analysis"?
Cheers.
On 8 May 2009, at 14:58, Marc Dubin wrote:
> Dear All,
>
> I have a TBSS & linear regression question.
>
> I have run a simple linear regression with one independent
> (cognitive test score) and one dependent variable (fractional
> anisotropy) that I set up in GLM_gui.
>
> EV1 = constant
> EV2 = cognitive test score (which is demeaned by GLM_gui)
>
> contrast of interest (contrast 2) is (0, -1)
>
> The problem is I get almost the same exact region of significance as
> I get in a different, more direct, manual FA analysis. However, with
> the manual approach, the correlation is positive, not negative. Does
> anyone have ideas about what might be giving rise to this sign error?
>
> Thanks in advance!
>
> Best,
> Marc
>
> On Wed, Jan 21, 2009 at 8:44 AM, Steve Smith <[log in to unmask]>
> wrote:
> Ah, good point. I was thinking more of the options where other
> programs were run _before_ bet2 as opposed to _after_.
>
> It _might_ be good enough to run bet2 with the mesh output option
> turned on, using as input the brain-extracted output from the first
> run of bet with the -S option. ??
>
> Cheers.
>
>
>
> On 20 Jan 2009, at 18:11, Marc Lalancette wrote:
>
> Thanks for your prompt reply.
>
> I suspect that for you the easiest thing
> would be to amend the -S option so that it gave the surface outputs
> you need, and then run the betsurf second-stage stuff separately
> afterwards."
>
> I looked at the script, but I don't know how to do that. The -S
> option
> first runs bet2, then applies corrections to the masks with fslmaths
> calls.
> If I add the option to output the surface meshes in the bet2 call, I
> would
> get the same mesh as without the -S option.
>
> Is there a tool I can use to convert a mask to a mesh directly? Or
> is that
> code only in bet2?
>
> Cheers,
> Marc Lalancette
>
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
>
>
> --
> Marc Dubin, MD PhD
> Clinical Research Fellow
> Brain Imaging Laboratory
> NYSPI & Columbia University
>
> Office: 212-543-6702
> Mobile: 646-831-8886
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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
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