Dear FSL experts
I would like to use PALM on some cortical thickness measures from freesurfer and was hoping that someone could look over my design matrix/command and let me know if it is appropriate?
I have two groups of participants (EV1, EV2) who have been scanned at 2 time-points (T1, T2). I am looking to use PALM to compute the main effect of change in IQ (EVs 7+8 below) on cortical thickness (.mgh) while controlling for age (EVs 3+4), and total cortical volume (EVs 5+6). I would also like to determine whether this relationship differs between the two groups as well as determining if thickness differs while controlling for everything else. I followed the basic outline of the two Groups with continuous covariate interaction in the GLM wiki and just wanted to make sure I have set up the following correctly:
Design Matrix:
EV1 EV2 EV3 EV4 EV5 EV6 EV7 EV8
1 0 28.2 0 981438.3 0 39 0
1 0 38.5 0 1001527 0 40.05556 0
1 0 35.6 0 1015722 0 48.80645 0
1 0 41.7 0 1112665 0 33.625 0
1 0 39.8 0 1087298 0 20.51351 0
1 0 44 0 1148600 0 16.625 0
0 1 0 34.7 0 1073384 0 33.42424
0 1 0 44 0 1163399 0 39.20513
0 1 0 31.18 0 1019120 0 48.34615
0 1 0 29.54 0 956024 0 35.57692
0 1 0 28.19 0 1049779 0 73.89655
0 1 0 30.49 0 941737.5 0 36
Contrasts:
grp1>grp2 1 -1 0 0 0 0 0 0
grp2>grp1 -1 1 0 0 0 0 0 0
Pos. slope grp1 0 0 0 0 0 0 1 0
Neg. slope grp2 0 0 0 0 0 0 -1 0
Pos. slope grp1 0 0 0 0 0 0 0 1
Neg. slope grp2 0 0 0 0 0 0 0 -1
grp1>grp2 slope 0 0 0 0 0 0 1 -1
grp2>grp1 slope 0 0 0 0 0 0 -1 1
Call to PALM:
palm –i lh.thickness.fsaverage.mgh -d matrix.csv -t contrasts.csv -o LH_thickness -fdr –n 10000 -corrcon -nouncorrected
Is this correct? Being that there are two groups should I also use the –vg option to define two variance groups, and does this also require a –eb input?
I would also like to run the analysis with lh and rh combined. I see that the command palm_hemimerge can be used for this, is it compatible with .mgh files?
Any help would be appreciated thanks!
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