I'm sorry -- I still don't follow what you mean by the "histogram fits". Is
this a GUI feature? I ran melodic from the command line. Is there somewhere I
can find this plot in the HTML report?
On Sunday, October 09, 2011 18:16:10 you wrote:
> Hi,
>
> In the first instance simply look at the histogram fits (click on the
> thresholded maps and then scroll to the bottom). The main Gaussian should
> be centred at zero and have unit standard deviation. If you happen to have
> really unusual data then the mixture model might not work, though - feel
> free to upload your filtered_func data and we'll have a look hth
> Christian
>
> On 6 Oct 2011, at 20:59, Benjamin Kay wrote:
> > 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)
> >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >> ------------------------------------------------------------------------
> >> ---
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