Hi,
Yes, unless you change the default settings the number of components
is controlled via an initial PCA as described in the paper and
technical report (have we not had this discussion before?). The
threshold parameter is unrelated to all this - it relates to the way
that the spatial IC maps get thresholded when using the Gaussian/
Gamma mixture model in order to perform an alternative hypothesis
test: voxels with a larger posterior probability of 'activation' are
shown.
cheers
Christian
On 30 Apr 2007, at 23:22, Xuelin Cui wrote:
> Christian:
>
> Thanks. With your reply and the melodic _slices, I have more sense
> about ICA on fMRI now. One more question: Is the number of the
> independent components controlled by preprocess PCA? There is a
> parameter that I can modify in MELODIC, threshold. Is that
> parameter for controlling the summation of eigenvalues in PCA? Thus
> the number of IC afterwards?
>
> Thanks a lot
>
> Xuelin
>
> ****************************************
> Xuelin Cui
> Department of Electrical Engineering
> University of Hawaii-Manoa
> Honolulu HI 96822
>
> Tel: 1-808-349-0983
> Email: [log in to unmask]
> ****************************************
>
> ----- Original Message -----
> From: Christian Beckmann <[log in to unmask]>
> Date: Monday, April 30, 2007 4:00 am
> Subject: Re: [FSL] a question on IC map and time course
> To: [log in to unmask]
>
>> Hi
>>
>> I do not understand why you start talking about slices - the rest
>> is
>> bbasically right.
>> cheers
>> c
>>
>>
>>
>>
>> On 30 Apr 2007, at 14:50, Xuelin Cui wrote:
>>
>>> Christian:
>>>
>>> Thanks for your reply.
>>>
>>> According to your last Email, can I understand the spatial map
>> and
>>> the time course for a single component as follows: Those spatial
>>> maps of a single IC is aquired at same time, but from different
>>> slices. The spatial map of an single IC is for all the time
>> points
>>> during the scan. The corresponding time course is for controlling
>>
>>> how the spatial map contribute to the fMRI signal at each time
>> points.>
>>> Am I right?
>>>
>>> Thanks a lot
>>>
>>> Xuelin
>>>
>>> ****************************************
>>> Xuelin Cui
>>> Department of Electrical Engineering
>>> University of Hawaii-Manoa
>>> Honolulu HI 96822
>>>
>>> Tel: 1-808-349-0983
>>> Email: [log in to unmask]
>>> ****************************************
>>>
>>> ----- Original Message -----
>>> From: Christian Beckmann <[log in to unmask]>
>>> Date: Monday, April 30, 2007 7:53 pm
>>> Subject: Re: [FSL] a question on IC map and time course
>>> To: [log in to unmask]
>>>
>>>> Hi,
>>>>
>>>> On 30 Apr 2007, at 08:54, Xuelin Cui wrote:
>>>>
>>>>> hi folks:
>>>>>
>>>>> I ran MELODIC for fMRI data, and thus have a bunch of
>>>> independent
>>>>> components which are displayed by a html file. In the html file,
>>>>
>>>>> there is a spatial map, a time course, as well as a Fourier
>>>>> spectrum of the time course.
>>>>>
>>>>> I have some questions on those in the html file:
>>>>>
>>>>> 1. Are all the spatial maps in single html file snapped at
>>>>> different time point? IF so what time are they?
>>>>>
>>>> No
>>>>
>>>>> 2. What is the relation between the time course and the spatial
>>>> map
>>>>> in the same html file?
>>>>>
>>>>
>>>> They express the spatial and temporal characteristics of a
>>>> component
>>>> - in a similar way that EVs (regressors in the GLM) and the
>>>> associated maps of parameter estimates express BOLD modulation.
>>>> That
>>>> is, the spatial maps corresponds to a map of parameter estimates
>>>> and
>>>> the time course describes how that spatial map is modulated in
>>>> strength at different time points.
>>>>
>>>>> 3. Are the 125 points time course variance corresponds to a
>>>> certain
>>>>> voxel in the brain? If so, which voxel is it? If not, what is it
>>>>
>>>>> related to? Some certain region?
>>>>>
>>>>
>>>> Likewise, the time course is related to the entire IC map - not to
>>>> a
>>>> single voxel.
>>>> cheers
>>>> christian
>>>>
>>>>> Thanks a lot
>>>>>
>>>>> Xuelin
>>>>>
>>>>> ****************************************
>>>>> Xuelin Cui
>>>>> Department of Electrical Engineering
>>>>> University of Hawaii-Manoa
>>>>> Honolulu HI 96822
>>>>>
>>>>> Tel: 1-808-349-0983
>>>>> Email: [log in to unmask]
>>>>> ****************************************
>>>>
>>>> ____
>>>> Christian F. Beckmann
>>>> University Research Lecturer
>>>> Oxford University Centre for Functional MRI of the Brain (FMRIB)
>>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
>>>> tel: +44 1865 222551 fax: +44 1865 222717
>>>>
>>
>> ____
>> Christian F. Beckmann
>> University Research Lecturer
>> Oxford University Centre for Functional MRI of the Brain (FMRIB)
>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
>> tel: +44 1865 222551 fax: +44 1865 222717
>>
____
Christian F. Beckmann
University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
[log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
tel: +44 1865 222551 fax: +44 1865 222717
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