After image registration, FSL gives 4x4 matrix among which the 4th column is translation parameters. Are they in mm scale or what's the way to cenvert them in mm scale?

Farhana,

You may have better luck with a tool-specific question on that tool's discussion list, in this case FSL's mailing list at http://www.jiscmail.ac.uk/lists/fsl.html

Best,
Christian

Hi Farhana,

Some general comments (not specific to FSL/flirt):

An affine transformation with the translation parameters in the fourth column, [A|t], can be factored into a product of homogeneous 4x4 matrices, [I|t][A|0]. This means that the translation can be considered to happen after the scalings (and rotations, skews), and therefore has the units of the output coordinates. So, yes, typically translations will be in mm.

However, scaling, rotation and shear change the coordinates of all points other than the origin. If this origin is not what you would intuitively consider the image centre, then be very careful trying to interpret the translation parameters. For example, if the origin is the first voxel stored (I think this is true for FSL), then a voxel somewhere in the middle of the brain will be swung around by a rotation (sorry, this would be clearer with a figure!), so the translation parameters will not be what you might visually estimate would be needed to align e.g. your image's AC with that of the MNI template.

I hope that makes sense,
Ged

Quick clarification of my previous message:
[A|t], [I|t] and [A|0] are intended to illustrate the partitioning of the 3x4 block of the homogeneous matrices into a 3x3 rotation/scale/skew component and a 3x1 translation component; the 1x4 block of:
[0 0 0 1]
which is present in all affine transformations represented in homogeneous forms is implicit.

Ged.