Hi
On 1 May 2007, at 06:39, Xuelin Cui wrote:
> hi
>
> One more question:
> If we see the melodic_slices.pdf, page 16, can I say the time
> courses extracted from fMRI data are the columns in the mixing
> matrix. And, each row in component matrix is actually a spatial map?
>
yes
> If so, what the value of the fourier spectrum for a single time
> course? Since time course is besically some weights that modulates
> the spatial components anyway.
>
This is the power spectrum of the time course - useful for e.g. block
designs where the power spectrum should peak at the fundamental
frequency of your design
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]
> ****************************************
>
> ----- Original Message -----
> From: Christian Beckmann <[log in to unmask]>
> Date: Tuesday, May 1, 2007 6:54 am
> Subject: Re: [FSL] a question on IC map and time course
> To: [log in to unmask]
>
>> 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
>>
____
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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