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FSL  July 2008

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Subject:

Re: Melodic output questions

From:

"Christian F. Beckmann" <[log in to unmask]>

Reply-To:

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

Date:

Mon, 28 Jul 2008 22:46:05 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (107 lines)

Hi

On 25 Jul 2008, at 19:42, Michal Kuniecki wrote:

> Hello,
>
> 	Customarily I would like to begin with being sorry for asking
> question which has high probability of being trivial to well ......
> Christian Beckmann for example :-) But anyway I haven't found straight
> answer for it neither on the list nor in the documentation.
> 	
> 	Basically I would like to understand MELODIC output better. I
> perform Tica analysis on my data additionally specifying both box-car
> function (I use simple ABAB block design for all subjects) and between
> subject contrast. In the output which I get if one clicks at the graph
> representing the timecourse of the particular component one gets an  
> array of
> numbers. As I understand they represent the timecourse associated with
> particular component separately for each subject (also the  
> timecourse and
> the model fit are given in first two columns).

Yes, the final N columns are the time courses for each one of the  
input data sets, the first column is the rank-1 approximation of these  
N time courses and (if a design was included in the GUI) a further  
column (2nd) shows the full model fit of the design.mat to the rank-1  
approximation.

> I do not understand however
> what is the unit or metrics behind those numbers (I understand that  
> they are
> normalized, but normalized what?).
> 	

The time courses (1st column in t??.txt) are normalised to unit  
standard deviation and all the energy is absorbed into subject/session  
mode vectors. The data is kept on the original scale (typically unit- 
less gray value intensities that come off your scanner)


>
> 	Similarly in "Session/Subjects mode" we get boxplot accompanied by
> another plot representing, as I get it goodness of fit between  
> particular
> subject and the timecourse of the particular component. But again,  
> how is
> this synthetic measure being calculated and what does it precisely
> represent?

The session/subject mode is calculated from the selection of all time  
courses via the rank-1 approximation. The boxplot again is on an  
almost arbitrary scale - it is still useful to judge if a component is  
non-zero for all the individual subjects or if the component is an  
'outlier' component (i.e. has one or only few very strong subjects and  
the remaining ones close to 0). If no between-subject model has been  
included then by default melodic will simply test for average group  
effect (i.e. use a constant 1 regressor to see if on average the group  
activated). If a group design has been specified, melodic will  
calculate a between-subject GLM using the specified design, e.g.  
testing for group differences using an unpaired or paired t-test.

>
>
> 	Additionally I would like to ask if it is sound and reasonable to
> import the data representing timecourses for particular subjects for
> particular component (those described in second paragraph) aggregate  
> them
> for rest and active condition (that is in case of my simple ABAB  
> design) and
> perform standard GLM analysis on them (in my case I would have  
> repeated
> factor of condition 2 levels and between subjects factor of gender 2  
> with
> levels). I'd like to do this GLM in order to get some more insight  
> into the
> between subject effects other than this synthetic measure provided in
> session/subject mode and COPE estimates.
>

Yes, that's reasonable but might be a lot of work  depending on how  
you do it. If you specify a group design, melodic already does what  
you're proposing on the rank-1 time courses. If you'd like to test  
every single (subject specific) time course separately then the  
easiest thing to do is to run fsl_glm

fsl_glm -i t??.txt -d design.mat -c design.con -o output.txt

will do what you want for every single column in t??.txt
hth
Christian



> Best regards
> Mike
>
> Michal Kuniecki
> Jagiellonian University
> Institute of Psychology
> Dpt. of Psychophysiology
> ul. Ingardena 6, room 605
> 30-060 Krakow, Poland
>
>
>
> 	

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