Hi Peter,
> I've collected resting-state fmri data from a patient group and a
> control
> group. After processing the data using the pre-stats tab in FEAT and
> subsequently running MELODIC, I merged the subjects' melodic outputs
> together and reran MELODIC. From the resulting output, I've
> indentified a
> number of components of interest that I'd like to compare between
> the two
> groups.
> My understanding of what I should do is the following:
>
> 1) Create a mask representing the combined thresh_zstat maps for
> both groups.
nothing wrong with this, but you won't need it later
> 2) Concatenate all the thresh_zstat maps of a particular component
> for all
> subjects, with all the subjects in one group first, followed by all
> the
> subjects in the second.
>
No, you wouldn't want to run any model based higher-level analysis on
thresholded lower-level stats images - simply use the associated
unthresholded maps instead.
> 3) Create design.mat and design.con files using the GLM Setup utility,
> where my design looks like the following:
> group EV1 EV2
> groupA groupB Title EV1 EV2
> s1 1 1 0 | C1 groupA mean 1 0
> s2 1 1 0 | C2 groupB mean 0 1
> s3 1 1 0 | C3 A > B 1 -1
> s4 1 1 0 | C4 B > A -1 1
> s5 2 0 1 |
> s6 2 0 1 |
> s7 2 0 1 |
> s8 2 0 1 |
>
That sounds OK
> 4) run a Two-Sample Unpaired T-test using RANDOMISE with the following
> command:
>
> randomise -i <4D_input> -o <output> -d design.mat -t design.con -c
> 0.99
>
nope, the argument to the -c (or -C) option is in units of the raw t-
stats (not z) that is being formed within randomise, i.e. if you want
a cluster forming threshold of t>2.3 use that number here. The output
file contains the p-values, i.e. you can threshold that one at 0.99,
say after having obtained it from randomise.
hope this helps
christian
> Here are my questions:
> Does it appear I am setting up the design correctly?
> Is using the option "-c 0.99" the equivalent of looking for
> significance
> at p<0.01?
> Do you have any other suggestions or recommendations for carrying
> this out?
>
> You help is greatly appreciated. Thanks in advance.
>
> Cheers,
>
> Pete
>
> Center for Magnetic Resonance Research
> University of Minnesota
____
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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