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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! ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1