Different size of files after alignment with “-giant_move” option


I’ve got this error message when using 3dttest++:

ERROR: Option -setA: dataset ‘XXX’ does not match first one in size

  • ‘XXX’ has 151552 voxels, but first one ‘YYY’ has 458575 voxels

and found that the difference in size depends on alignment option used in align_epi_anat.py. The XYZ dimension are as follows: original data – 64x64x37; after align with “-giant_move” option – 65x83x85; align without “-giant_move” or with “-big_move” option does not change the original data size.

I assume that the script (when using “-giant_move” option) “make some space” for shifting and rotating the image, so it results in bigger file.
My question is, whether it always resize the image the same way, i.e. does the result will always have 65x83x85 size?

For most of my data, “-giant_move” option works best. Thus, I need to match the rest to have the same size. My first idea is to use “3dZeropad -RL 65 -AP 83 -IS 85 (…)”. Is it correct, or you would recommend something else?
Or maybe there is a way to resize them back after alignment? For example to remove slices/voxels with “zeros” that are outside the brain? This actually would be a better option, because using “-giant_move” makes files almost 2 times bigger…


The giant_move option moves the data into the space of the target with a voxel resolution of the minimum dimension of the input dataset. If you want something else, use the “-master_…” options.