On Thursday, October 06, 2011 14:29:41 you wrote:
> Hi - why do you think the values in melodic_IC are too high? These should
> be valid Z values and are probably what you want to be working with.
Thank you for responding! In the melodic practical, the example uses fslview
to look at melodic_IC with "-b 5,10", so I had expected my z-values to be
somewhere in this range. Instead I have a great many z-values greater than 50.
To see my component clearly I have to use "-b 150,300". (When looking at
melodic_oIC, I can see clean-looking components with "-b 0.3,1".) My
probability maps light up pretty much the entire brain, even with "-b 0,0.99",
when melodic is run with the default --mmthresh=0.5.
> The
> thing to check is that the central Gaussian (null part of the histogram)
> is of standard devation 1. I'll be surprised if this is wrong - you're
> just not used to seeing strong signal (the tail) relative to such a
> cleaned-up null (because the structured noise is moved into the other
> components and not appearing in the null).
I'm sorry, but could you please explain how I can check this?
> Cheers.
>
> On 6 Oct 2011, at 14:58, Benjamin Kay wrote:
> > Bump! If you know how melodic_IC is derived from melodic_oIC, please
> > share! I'm having trouble with a dataset where the z-values in
> > melodic_IC are way too high. Knowing what's supposed to happen would be
> > very helpful to me in my efforts to debug this.
> >
> > On Wednesday, September 28, 2011 12:21:38 you wrote:
> >> It's been mentioned before that melodic_oIC contains the "raw" IC maps,
> >> that melodic_IC contains the Z-scaled IC maps, and that Noise_stddev_inv
> >> is used to convert the former to the latter. I'm curious as to precisely
> >> how this conversion is achieved. That is, given melodic_oIC, how do I
> >> get melodic_IC? The IEEE TMI paper seems to suggest it is a simple
> >> matter of doing voxel-wise division of each raw IC map by the standard
> >> deviation of the noise (technically the square root of the estimate of
> >> the noise variance), so:
> >> http://www.fmrib.ox.ac.uk/analysis/techrep/tr02cb1/tr02cb1/node8.html
> >>
> >> fslmaths melodic_oIC -mul Noise_stddev_inv my_melodic_IC
> >>
> >> But this doesn't seem to work. Indeed, lines 519-548 of meldata.cc would
> >> suggest something more is happening. Can anyone explain how to get
> >> melodic_IC from melodic_oIC using fslmaths?
>
> ---------------------------------------------------------------------------
> 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)
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