I am in the unfortunate position of having received a ROI in 3x3x3mm space, which is not the space of my data - I'd like to get this ROI into 2x2x2 standard space, once it's there I know what to do with it.

Added complication: I don't have ANY 3x3x3 brains on hand. To make our lives easier for my first attempt, let's assume that the space we're looking for is just a downsampled version of the MNI standard brain. (If it's not, I will need to get my hands on the source data, but if that were easily done I wouldn't be here.)

How do I go about converting the ROI into 2x2x2 space? Obviously, I need to preserve its location as best as possible. I tried to start out by downsampling a standard brain via:

flirt -interp nearestneighbour -in bg_image -ref bg_image -applyisoxfm 3 -out 3bg_image -omat 3mm_to_2mm.mat.

My hope was I could then put that transformation matrix into:

flirt -in <3mm ROI> -out <2mm ROI> -ref <standard brain> -applyxfm -init 3mm_to_2mm.mat.

Unfortunately, my first flirt command changes around the spatial dimensions, not just the voxel counts. It goes down to 2x2x2 but the space goes from 91x109x91 (standard bg_image) to 60x72x60, while my ROI is 48x64x48. So, I'm clearly missing something here.

Anyone know how to accomplish this?

Thanks!

-----
Benjamin Philip, Ph.D.
Postdoctoral Fellow - Freylab
University of Missouri
206 Melvin H. Marx Bldg
1416 Carrie Francke Drive
Columbia, MO 65211
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