Dear experts,

I'm attempting to run a longitudinal analysis of hippocampal shape changes in PALM, where the baseline scan is entered as a per-voxel regressor. For input, I specify a 4D nifti file of hippocampus shape at follow-up (calculated from the concatenated .bvars using first_utils). For the per-voxel regressor, I specify a similar 4D nifti file but now at baseline. In my design.mat file I specify 8 EV's (not including the baseline per-voxel regressor). My contrast file has 8 contrasts, one for each EV in the design file.

palm -i {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-r-hipp-scaled.nii ...
-m {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-r-hipp-scaled-mask.nii ...
-evperdat {path}/Desktop/r-hipp-vertex/regression-scaled/pvr-match-r-hipp-scaled.nii  9 1 ...
-o {path}/Desktop/r-hipp-vertex/regression-scaled/palm ...
-d {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-design.mat ...
-t {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-tcontrast.con ...
-demean -T -C 2.3 -n 1000

My first question is: how do I specify the extra per-voxel regressor in my design and contrast files?

If e.g. I should add an extra column in the design.mat file, what should this column consist of? I've tried changing numWaves/numContrast/matrices to 9 instead of 8 in many different combinations, but PALM keeps giving me the reshape-error.

My second question is: can I specify a new mask for the baseline-scans after the -evperdat line?

I've attached my design and contrast files (at this point with just the 8 other predictors). The design file is a .txt file because my email server won't send it as .mat . Thank you very much for your help!

All my best,
Lizanne