Hi David,
Note that fslcc includes ALL voxels in its calculation of the spatial
"correlation" including voxels with 0's outside of the brain. In my
opinion, this is not a meaningful estimate of the true spatial
correlation.
cheers,
-MH
On Thu, 2012-02-02 at 07:40 +0000, Stephen Smith wrote:
> Hi - I'm not sure which analysis you're referrring to, but for simply
> matching up maps (as opposed, for example, to doing a dualregression),
> yes we would probably just use fslcc
>
>
> Cheers.
>
>
>
>
>
> On 1 Feb 2012, at 18:33, David V. Smith wrote:
>
> > OK, great -- thanks for both sets of images! Can you also verify
> > that one of the methods below is the way you guys perform the
> > spatial cross-correlation?
> >
> > fsl_glm -i IC01.nii.gz -d PNAS_Smith09_rsn10_3mm.nii.gz -o PE --
> > out_z=z_score -m mask.nii.gz
> > where IC01.nii.gz is just the first image in the melodic_IC image
> > (fslroi melodic_IC.nii.gz IC01 0 1)
> >
> >
> > And then report the PEs as the correlation estimates? This method
> > seems odd because of the extremely high z-scores and PEs aren't
> > explicitly r values for a correlation...
> > [smith@node52 groupICA_AU]$ more PE
> > 0.24856 0.437975 -0.135177 -0.0728717 0.0331276 -0.0438093
> > -0.0734834 0.0104588 0.0270564 0.0727842
> > [smith@node52 groupICA_AU]$ more z_score
> > 91.2948 141.214 -41.624 -25.2608 10.92 -13.4459 -20.1861
> > 3.80642 9.4519 24.6514
> >
> >
> > Or did you guys use fslcc?
> > fslcc RSN02.nii.gz IC01.nii.gz (in the 3rd column, this has 0.46 as
> > the correlation)
> > where RSN02.nii.gz is the second image in the RSN template image
> > (fslroi PNAS_Smith09_rsn10_3mm.nii.gz RSN02 1 1)
> >
> >
> > If both methods are valid, is one preferred over the other?
> >
> >
> > Thanks again!
> >
> >
> > Cheers,
> > David
> >
> >
> >
> >
> >
> >
> > On Feb 1, 2012, at 12:02 PM, Stephen Smith wrote:
> >
> > > Hi - Christian has put this online now:
> > > http://www.fmrib.ox.ac.uk/analysis/royalsoc8/
> > > Cheers.
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On 1 Feb 2012, at 08:26, Stephen Smith wrote:
> > >
> > > > Hi, the RSN/BrainMap images are at
> > > > http://www.fmrib.ox.ac.uk/analysis/brainmap+rsns/
> > > > We were going to put the Beckmann 05 images on there as well -
> > > > haven't gotten around to that yet…
> > > > Cheers
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On 1 Feb 2012, at 06:58, David V. Smith wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Did these RSN template maps (from the 2005 Beckmann paper?)
> > > > > ever get posted to the web? I can't find any other mention of
> > > > > it on the forums, and I'm not exactly sure where to look on
> > > > > the FMRIB site.
> > > > >
> > > > >
> > > > > Thanks!
> > > > > David
> > > > >
> > > > >
> > > > >
> > > > > On Sep 6, 2011, at 12:13 PM, Stephen Smith wrote:
> > > > >
> > > > > > Hi - we've been meaning to put the brainmap/RSN PNAS maps up
> > > > > > on the web for a while but keep not getting around to it -
> > > > > > we'll try to get these up by the end of September.
> > > > > > Cheers.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 2 Sep 2011, at 06:37, Eva Kenny wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > > I was planning on using the template matching procedure on
> > > > > > > my Melodic data to identify ICs of interest and wondered
> > > > > > > if there were template RSNs available?
> > > > > > > Many thanks,
> > > > > > > Eva
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > > ---------------------------------------------------------------------------
> > > > > > 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
> > > > > > ---------------------------------------------------------------------------
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > > ---------------------------------------------------------------------------
> > > > 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
> > > > ---------------------------------------------------------------------------
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > > ---------------------------------------------------------------------------
> > > 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
> > > ---------------------------------------------------------------------------
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
>
>
> ---------------------------------------------------------------------------
> 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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