Thanks Christian:)
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 3:15 pm
Subject: Re: [FSL] a question on IC map and time course
To: [log in to unmask]
> 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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