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Subject:

Re: Concatenate run/session or not?

From:

Stephen Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 9 Sep 2004 16:21:05 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (155 lines)

Hi,

On Mon, 6 Sep 2004, X Liu wrote:

> Thanks very much. I thought the original question is going to be buried
> without being answered. I've done Approach 1 and am holding to re-do it
> with Approach 2 until I get some expert opinion on it. The second approach
> definitely requires more labor. Are there any strong reasons against the
> first approach (e.g. statistical validity, filter efficiency, motion
> correction across runs, etc.)? I will go ahead and anlyze the data with
> Approach 2 and see how much the end results differ.

Yes - there's various comments in the FSL email archive on this. Time
series concatenation is nasty as the 1D signal doesn't "join up" well
across runs, with nasty analysis implications....

> P.S. Another message (Distributed Computing Once More) I sent on Aug. 30
> did not get people involved to discuss. Hopefully FSL development team and
> other experts on this issue can look into it to see if it is useful. One of
> the advantages of FSL is that it enables easy batch processing (mostly
> serially) with scripts. Batch parallel processing has to be able to run on
> distributed/clustered system to gain full power.

Yes, in the forthcoming release, the diffusion toolkit will use parallel
processing - for other areas like multi-session FEAT analysis or FLAME
runs, UCLA are doing some really nice work on this, so watch this
space....

Thanks, Steve.

>
> On Sat, 4 Sep 2004 09:21:50 +0100, Stephen Smith <[log in to unmask]>
> wrote:
>
> >Hi, yes that all makes sense. Approach 2 is what you want and you're right
> >to take out the constant-EV ev1 from your original email.
> >
> >Cheers.
> >
> >
> >On Tue, 31 Aug 2004, Xun Liu wrote:
> >
> >> On Tue, 31 Aug 2004 21:17:33 +0100, X Liu <[log in to unmask]>
> wrote:
> >>
> >> >Concatenate run/session or not?
> >> >
> >> >We have a design with 2 independent variables (IV1 and IV2), each with 3
> >> >levels. IV1 is manipulated across blocks within a run and IV2 is
> >> >manipulated across runs. There are two approaches I can think of to
> anaylze
> >> >the data for the main effects and interaction for this design. What is
> the
> >> >advantage and disadvantage of each approach, from the conceptual and
> >> >practical perspectives? Is one more valid than the other from the
> >> >statistics point of view? Thanks very much.
> >> >
> >> >
> >> >Approach 2:
> >> >Analyze each run separately and model just the 3 conditions/levels of
> IV1
> >> >(ev1, ev2, ev3). Then the main effects of IV1 can be set up as below.
> >> >
> >> >Contrast ev1 ev2 ev3
> >> >mean (1)  1   1   1
> >> >IV1  (2)  1  -1   0
> >> >     (3)  1   0  -1
> >> >     (4)  0   1  -1
> >> >
> >> >And then proceed to the group analysis with the EVs/contrasts setup as
> >> >below for the three levels of IV2 (say for 5 subjects)
> >> >
> >> >Group ev1 ev2 ev3 ev4 ev5 ev6 ev7 ev8
> >> >1      1   1   1   1   0   0   0   0
> >> >1      1   1   1   0   1   0   0   0
> >> >1      1   1   1   0   0   1   0   0
> >> >1      1   1   1   0   0   0   1   0
> >> >1      1   1   1   0   0   0   0   1
> >> >1      1  -1   0   1   0   0   0   0
> >> >1      1  -1   0   0   1   0   0   0
> >> >1      1  -1   0   0   0   1   0   0
> >> >1      1  -1   0   0   0   0   1   0
> >> >1      1  -1   0   0   0   0   0   1
> >> >1      1   0  -1   1   0   0   0   0
> >> >1      1   0  -1   0   1   0   0   0
> >> >1      1   0  -1   0   0   1   0   0
> >> >1      1   0  -1   0   0   0   1   0
> >> >1      1   0  -1   0   0   0   0   1
> >> >
> >> >Contrast ev1 ev2 ev3 ev4 ev5 ev6 ev7 ev8
> >> >c1        1   0   0   0   0   0   0   0
> >> >c2        0   1   0   0   0   0   0   0
> >> >c3        0   0   1   0   0   0   0   0
> >> >c4        0   1  -1   0   0   0   0   0
> >> >
> >> >Then the .gfeat folder should include 4 cope#.feat subfolders, one for
> each
> >> >of the contrasts from the first level. zstat2 to zstat4 of cope1.feat
> will
> >> >assess the main effect of IV2 (zstat1 is the overall grand mean of both
> IVs
> >> >again baseline). zstat1 of cope2.feat to cope4.feat will assess the main
> >> >effect of IV1. zstat2 to zstat4 of cope2.feat to cope4.feat will assess
> the
> >> >interactions.
> >>
> >> Just found out an error. To correct myself, ev1 is a linear combination
> of
> >> ev4 to ev8. So take out ev1 and contrast 1 is just the combination of the
> >> new ev3 to ev7 (weighted or not WRT to the other contrasts?). The
> >> interpretation of the main effects and interaction above stands.
> >>
> >> Group ev1 ev2 ev3 ev4 ev5 ev6 ev7
> >> 1      1   1   1   0   0   0   0
> >> 1      1   1   0   1   0   0   0
> >> 1      1   1   0   0   1   0   0
> >> 1      1   1   0   0   0   1   0
> >> 1      1   1   0   0   0   0   1
> >> 1     -1   0   1   0   0   0   0
> >> 1     -1   0   0   1   0   0   0
> >> 1     -1   0   0   0   1   0   0
> >> 1     -1   0   0   0   0   1   0
> >> 1     -1   0   0   0   0   0   1
> >> 1      0  -1   1   0   0   0   0
> >> 1      0  -1   0   1   0   0   0
> >> 1      0  -1   0   0   1   0   0
> >> 1      0  -1   0   0   0   1   0
> >> 1      0  -1   0   0   0   0   1
> >>
> >> Contrast ev1 ev2 ev3 ev4 ev5 ev6 ev7
> >> c1        0   0  0.2 0.2 0.2 0.2 0.2
> >> c2        1   0   0   0   0   0   0
> >> c3        0   1   0   0   0   0   0
> >> c4        1  -1   0   0   0   0   0
> >>
> >
> > Stephen M. Smith  DPhil
> > Associate Director, FMRIB and Analysis Research Coordinator
> >
> > Oxford University Centre for Functional MRI of the Brain
> > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> > +44 (0) 1865 222726  (fax 222717)
> >
> > [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>

 Stephen M. Smith  DPhil
 Associate Director, FMRIB and Analysis Research Coordinator

 Oxford University Centre for Functional MRI of the Brain
 John Radcliffe 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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