Also called a register.dat file, this file has the following format:

{{{subjectname
in-plane resolution(mm)
between-plane resolution(mm)
intensity
m11 m12 m13 x0
m21 m22 m33 y0
m31 m22 m33 z0
0   0   0  1
<float2int_method>}}}

where subjectname is the name of the subject as found in $SUBJECTS_DIR, in-plane resolution is the distance between adjacent rows or columes, between-plane resolution is the distance between adjacent slices, intensity is ignored, and the remainder is the 4x4 affine tranform that converts XYZ in the input volume to XYZ in the subject's anatomical space.