Dear Sally,
most likely, Ged's script does not resample your images to matching voxel sizes and orientations. Assuming that you are working on spatially normalised (wc/wp*) segmented images, you will still need to resample your ROIs to the same voxel size and orientation as the wc/wp images. There are many way to do that, the most convenient one may be using "Spatial->Realign->Reslice". There, you select first one of your wc/wp images as reference, followed by all your ROIs. As output option you may choose "Images 2..n". This will not rewrite your reference image, but create an r<ROI> image for each of your ROIs. Use the r<ROI> images then in the script.
Best
Volkmar
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