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FSL  October 2011

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Subject:

Re: convert melodic_oIC to melodic_IC

From:

Benjamin Kay <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 10 Oct 2011 07:40:54 -0400

Content-Type:

Multipart/Mixed

Parts/Attachments:

Parts/Attachments

Text/Plain (124 lines) , IC_19_MMfit.png (124 lines)

Ah, there it is! Don't I feel rather foolish now (^_^')

The center of the histogram is close to zero and the peak is farily narrow. 
Does the attached image look typical to you?

Means : -0.000000 85.754878 -53.936238
Vars : 1.000000 2774.603215 2125.397460
Prop. : 0.561720 0.204818 0.233461 

On Monday, October 10, 2011 02:00:47 you wrote:
> Yes, you can:
> click on the tresholded image - that should bring you to a second page -
> then scroll down to see the GGMM fit.
> Cheers,
> Andreas
> 
> Am 10.10.11 00:35 schrieb "Benjamin Kay" unter <[log in to unmask]>:
> >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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