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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