Memory consumption in transformix

Sometimes you want to work on memory constrained systems, even with (medical) imaging data that is quire large. This page gives an overview of the memory consumption of transformix, and some tips on how to reduce it. Much of it also holds for elastix.

The default memory consumption of transformix

For resampling an image several components need memory:

• The moving image, i.e. the image that is to be deformed. This is stored with an InternalImagePixelType, which can be set by the user in the TransformParameters file.
• The interpolator. The BSplineInterpolateImageFunction precomputes some coefficients, which are stored in a double image the size of the moving image.
• The resampled image itself, usually of the size of the fixed image. This is again stored with an InternalImagePixelType. To get a user-defined pixel type one can set the ResultImagePixelType in the TransformParameters file. If this is different from the InternalImagePixelType, a cast is performed between the types, consuming another piece of memory.

For example: Say we have a 512^3 short image as input, which is resampled to a 512^3 short image. So both images are 512^3 x 2 byte = 256 MB. Then the memory consumption is given by:

what	how much	Setting 1	Setting 2	Setting 3	Setting 4
		internal = short, interpolator 1	internal = float, interpolator 1	internal = short, interpolator 2	internal = short, interpolator 3
moving image	1 x moving size x internal	256 MB	512 MB	256 MB	256 MB
interpolator 1	1 x moving size x double	1024 MB	1024 MB
interpolator 2	1 x moving size x float			512 MB
interpolator 3	0				0 MB
resampled image	1 x fixed image x internal	256 MB	512 MB	256 MB	256 MB
output image	1 x fixed image x output type	0* MB	256 MB	0* MB	0* MB
total		1.5 GB	2.25 GB	1.0 GB	0.5 GB

* If the resampled image and the output image are of the same type no casting is performed
interpolator 1 = B-spline interpolator with a double coefficient image internally
interpolator 2 = B-spline interpolator with a float coefficient image internally
interpolator 3 = A nearest neighbour or linear interpolator, which uses no internal coefficient image

What can you do to save memory?

1. The B-spline interpolator is the main consumer, because it uses an internal coefficients image of type double. You can instead select (Interpolator "BSplineInterpolatorFloat"), which stores this internal image in float format. This would reduce memory consumption by 512 MB for the example.

2. If you were to use the LinearInterpolator or NearestNeighborInterpolator the internal image is completely omitted. This would reduce memory consumption by 1 GB for the example. Note however that linear or nearest neighbor interpolation will degrade the results a little, compared to cubic B-spline interpolation.

3. Change the InternalImagePixelType from float to short. This saves you 3 times a short image, i.e. 0.75 GB for the example. This will also result in a little degradation.