Hi All,
I’ve been reading through past threads about using melodic at a group level and just want to
make sure I understand what needs to be done, as I am new to using melodic like this. We have a
number of subjects, each of whom has 6 functional scans of the same task. We are interested in
determining which areas on average co-activate with a single region of interest, and also want to
investigate whether the ICAs associated with that ROI will vary with another continuous variable
(such as age) across subjects. Based on past threads, I think we need to do the following:
1) Run melodic on each individual scan.
2) Select ICAs that include our region of interest (except for those that are obvious noise).
3) Do avwsplit and avwmerge to merge those ICAs of interest into a single 4D file for each scan.
4) Move all the functional data into common space using flirt to create the transformation
matrix and applyxfm4D to apply it.
5) Run flame –cope=4Ddata –vc=4Ddata –mask=mask –ld=stats –dm=design.mat –
cs=design.grp –tc=design.con –jols
Is this correct so far?
My questions are:
1) Since we obviously did not do a first level FEAT with the task paradigm outlined in the stats,
what exactly will be the output of the flame? Will it find the average of the ICAs? Does it matter if
there are different numbers of ICAs for each scan?
2) Once we have run that second level flame (one for each subject) as –jols, will the correct files
(i.e. copes etc.) be created so that we will be able to perform the flame across subjects in the gui?
If not, how would we proceed to the next step? Will we be able to see how certain ICAs are or are
not present on average as a continuous variable changes across subjects?
3) I saw that some threads talk about using the Zstats images. Should we be using those
instead of the 4D concatenated files to do what I want to do? If so, how?
4) In the command applyxfm4D that was suggested for bringing the 4D file into common space,
what is the –singlematrix for?
Sorry for the long email. I just want to make sure we get it right.
Thank you for your help with this!
Best,
Meredith
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