>can find this plot in the HTML report
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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