Hi everybody,
I'm trying to perform VBM analysis using FSL.
I've successfully set up everything for my vbm analysis using FSL,
such as placing all the files in the same directory and re-scaling
the intensity values.
But at am stuck at setting up the design and contrast matrices.
I have 3 groups named control, short and long. Each group has 9
subjects.
I've been using the GLM setup GUI and have selected the higher level/
non-time-series analysis and told it there are 27 inputs.
I've assigned the first 9 inputs to group 1, the second 9 inputs to
group 2 and the final 9 to group number 3.
Am I correct that I need 3 EVs for this model? Do I then need to set,
for example, EV1 to 1 only for the 9 inputs in group 1 and likewise
for the other two groups?
Under the EV1, EV2 and EV3 labels in the GLM GUI there are text
boxes, what are these for?
The contrasts and F-tests tab defaults to "group mean" which I guess
is ok for functional analysis but not for a VBM analysis. Is there
even an equivalent for VBM analysis?
Are appropriate contrasts for this analysis control - short, control
- long and should I do F tests for each of these contrasts?
When I have 3 groups such as in this case do I need to use the -g
option to randomise when performing permutation testing?
Are the inputs read in the order in which they are concatenated in
the 4D file? So if fslvbm_3_proc concatenates in alphabetical order
will the first 9 inputs correspond to the first 9 volumes in the 4D
file which in this case will be the 9 control subjects? I'm assuming
that the next 9 volumes will be the 9 long subjects and the final 9
volumes the 9 short subjects. Does the order of the subjects within
group matter? So does EV1 correspond to the control group, EV2 to the
long and EV3 to the short groups?
I noticed that the fslvbm_1_bet defaults to passing -f 0.4 to BET. If
I run "fslvbm_1_bet -N -B -f 0.3" which option will bet use the 0.4
or 0.3?
Thanks in advance,
--
Dr Colm G. Connolly
School of Psychology and Institute of Neuroscience
The Lloyd Building
University of Dublin
Trinity College, Dublin 2, Éire
Tel: +353-1-896-8475
Fax: +353-1-671-3183
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