I couldn't get either of the built-in functions to work to check the registration between two volumes which should have been the same.

I also noticed that the tkregister2 wiki page contains no info about the command, though it does have a link to the TkRegister2 Guide, which does not exist.

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FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0

Kernel info: Darwin 10.6.0 i386

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swi> tkregister2 --targ SWI1.nii.gz --mov SWI2.nii --identity

tkregister_tcl /Applications/freesurfer/lib/tcl/tkregister2.tcl

ERROR: no registration file specified

swi> tkregister2 --targ SWI1.nii.gz --mov nsLGH_26Aug10_10.nii --check-reg

tkregister_tcl /Applications/freesurfer/lib/tcl/tkregister2.tcl

target volume SWI1.nii.gz

movable volume SWI2.nii

reg file /tmp/reg.tmp.1297311621.dat

LoadVol 1

ZeroCRAS 0

$Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $

Diagnostic Level -1

regio_read_register(): No such file or directory

Could not open /tmp/reg.tmp.1297311621.dat

ERROR: reading /tmp/reg.tmp.1297311621.dat