Hi,
On 14 May 2009, at 17:54, Marc Dubin wrote:
> Hi Steve,
>
> Thanks so much for getting back to me...
>
> The randomise command that I used is:
>
> randomise -i all_FA -o tbssFA_Elision_PN -m mean_FA_mask3000 -d
> designElision_PN.mat -t designElision_PN.con -n 5000 -V -x -D
>
> I have used this with and without the -1 option and with and without
> the -D option and get the same results.
Because the design matrix includes a mean EV you shouldn't demean the
data (so don't use -D option) and the -1 option also doesn't make
sense in this scenario. The rest looks fine. I take it you are
comparing the second contrast [0 -1] with the 'hand' approach below.
> I have also attached the design files.
>
> By manual, I mean the ROQS automatic segmentation technique
> developed by Niogi and McCandliss (Neuroimage, 2007, 35:166:174). I
> am using this to automatically isolate the left SCR by finding its
> boundary and then taking the average FA inside this boundary. This
> single number average correlates positively with my cognitive score.
I assume you are doing equivalent modelling - i.e. either demeaning
the data extracted in this way, or including a mean EV in your
regression?
> However, when I run the above FSL analysis, I get no positive
> correlation with any of the voxels in the left (or right) SCR.
> However, when I modify the FSL/TBSS analysis so the Elision contrast
> is (0 -1) instead of (0 1), I get voxels of significance throughout
> the entire left SCR , as expected, however these voxels are
> negatively correlated with the cognitive score (Elision). There
> seems to be a sign error somewhere.
Seems like there must be a dodgy step in this "hand" analysis....
Cheers.
>
> Any thoughts you have on what I'm doing wrong would be most
> appreciated!
>
> Best,
> Marc
>
> On Thu, May 14, 2009 at 9:18 AM, Steve Smith <[log in to unmask]>
> wrote:
> 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
>
>
> ---------------------------------------------------------------------------
> 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
> <Archive.zip>
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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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