The problem is probably that the image is outside of the tkregister2 FOV -- I noticed that there is a large shift from magnet isocenter in your image (about 30 cm). tkregister2 centers the FOV at isocenter. I still have not found a work-around for this, but you can use
mri_vol2vol --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mov orig.mgz --xfm transforms/talairach.xfm --o orig.tal.mgz
then
tkmedit fsaverage orig.mgz -aux ./orig.tal.mgz
to test out whether the transform is ok or not.
doug
Bum Seok Jeong wrote:
Hi!
I use axial LAS system 3D nifti and analyze format images to perform autorecon1 process. Skull stripping results looked fine. However, when I checked talairachs transform results (tkregister2 --mgz --s C1 --fstal), a part of original image was just shown at left upper corner and talairach template did not appear with white background. So I can not perform a manual registration. The message appeared as follows
Thanks in advance
bsJeong
<259> fs/tmp% tkregister2 --mgz --s C1 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1
%Wed Jan 3 12:24:29 2007>>> /bin/freesurfer/mni/bin/minctracc -clobber -debug /tmp/mritotal_16322/src_8_dxyz.mnc /bin/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_16322/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /bin/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -191.589493 222.719711 194.588959 -step 4 4 4 -tol 0.004 -simplex 2
talairach.xfm --------------------- 1.053 -0.003 -0.046 212.831; 0.006 1.123 0.061 -264.791; 0.045 -0.057 1.036 -186.491; 0.000 0.000 0.000 1.000; INFO: loading target /tmp/C1/mri/orig.mgzINFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 -62.500; 0.000 0.000 1.000 91.141; 0.000 -1.000 0.000 347.141; 0.000 0.000 0.000 1.000; INFO: loading movable /bin/freesurfer/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.053 -0.003 -0.046 212.831; 0.006 1.123 0.061 -264.791; 0.045 -0.057 1.036 -186.491; 0.000 0.000 0.000 1.000; subject = C1 Zoom Factor = 2 FOV = 256 Opening window C1 Setting scale tkregister2: interface: /bin/freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
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