Hi again,
> Okay. So, do I need to create a mask from this
> image, or just use the actual
> thresholded image?
Again, please follow the example I've given to you:
fslmaths ***_max_tfce_tstat*.nii.gz -thr 0.95 -bin
mask
> If I am creating a mask, is this
> not similar to creating
> an ROI for whatever given region?
Yes it is. Isn't it what you want when you ask for
"stat(ing) what the FA values (a)re for each group in
areas of significant difference"?
Cheers,
Gwen
> Thanks.
> David
>
> On Wed, Mar 5, 2008 at 8:48 AM, Gwenaëlle DOUAUD
> <[log in to unmask]>
> wrote:
>
> > Hi David,
> >
> > as indicated in the fslmaths command example, you
> > should use your p-values corrected for multiple
> > comparisons with the tfce, so something like
> > ***_max_tfce_tstat*.nii.gz and threshold this
> image to
> > get the significant results, so -thr 0.95.
> >
> > Cheers,
> > Gwenaelle
> >
> >
> > --- David Kideckel <[log in to unmask]> a
> écrit
> > :
> >
> > > Hi Gwen,
> > > Based on what you have said then, what image/s
> am I
> > > creating a mask from?
> > >
> > > David
> > >
> > > On Wed, Mar 5, 2008 at 7:33 AM, Gwenaëlle DOUAUD
> > > <[log in to unmask]>
> > > wrote:
> > >
> > > > Hi David,
> > > >
> > > > I think what Steve means is something like:
> > > > fslmaths your_tfce_max_tstatX_results -thr
> 0.95
> > > -bin
> > > > your_results_mask
> > > > then
> > > > fslmeants -i all_FA_skeletonised -m
> > > your_results_mask
> > > > -o mean_FA_results.txt
> > > >
> > > > Cheers,
> > > > Gwen
> > > >
> > > >
> > > > --- David Kideckel <[log in to unmask]>
> a
> > > écrit
> > > > :
> > > >
> > > > > Hi. Which cluster image should I use as the
> mask
> > > > > input to fslmeants? And
> > > > > what exactly do you mean by "also feed in
> > > > > all_FA_skeletonised"?
> > > > > Thank you.
> > > > > David
> > > > >
> > > > > On Wed, Mar 5, 2008 at 4:15 AM, Steve Smith
> > > > > <[log in to unmask]> wrote:
> > > > >
> > > > > > Hi, this is indeed a sensible number to
> > > report. If
> > > > > you use a given
> > > > > > cluster image as the mask input to
> fslmeants,
> > > and
> > > > > also feed in
> > > > > > all_FA_skeletonised, you can get the
> single
> > > > > cross-subject 'timeseries'
> > > > > > of mean FA over that mask - that should
> give
> > > you
> > > > > the numbers that you
> > > > > > want to report (including cross-subject
> error
> > > > > bars).
> > > > > >
> > > > > > Cheers.
> > > > > >
> > > > > >
> > > > > > On 4 Mar 2008, at 15:48, David Kideckel
> wrote:
> > > > > >
> > > > > > > Dear FSL Experts,
> > > > > > >
> > > > > > > I am almost finished running a TFCE and
> > > > > Randomise analysis for TBSS.
> > > > > > > Once this is done, what is the best way
> to
> > > > > prepare the data for a
> > > > > > > presentation. All I want to do is
> > > essentially
> > > > > state what the FA
> > > > > > > values were for each group (there are 3
> of
> > > them)
> > > > > in areas of
> > > > > > > significant difference.
> > > > > > >
> > > > > > > Thank you.
> > > > > > >
> > > > > > > David Kideckel, PhD Candidate
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>
---------------------------------------------------------------------------
> > > > > > 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
> <http://www.fmrib.ox.ac.uk/%7Esteve>
> > > <http://www.fmrib.ox.ac.uk/%7Esteve><
> > > > http://www.fmrib.ox.ac.uk/%7Esteve>
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>
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> >
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>
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