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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