Does it look flipped in tkregister2? If not, how are you judging that it is flipped? doug

On 05/11/2012 08:11 AM, Yosuke Morishima wrote:

Dear Freesurfer specialits,

I now have a problem that tkregister2 gives wrong orientation, specifically L-R orientation is flipped. I'm trying surface DTI fiber tracking by using FSL and Freesurfer as described in FSL documentation below and using tkregister2 to obtain transformation matrix from Freesurfer space to structural space. http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html

I got transformation matrix with the following command. tkregister2 --mov mri/orig.mgz --targ mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit

Apply this transformation matrix (freesurfer2struct.mat) to a freesurfer-space image, and then I got L-R flipped image in structural space.

I would really appreciate if you have any suggestions to solve the problem. Thanks.

Best wishes, Yosuke

Here is the message appeared in the terminal.

tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz movable volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz reg file junk LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -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; INFO: loading movable /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz 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 = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 -0.000; -0.000 1.000 0.000 0.000; -0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;

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---- Input registration matrix -------- 1.000 -0.000 -0.000 -0.000; -0.000 1.000 0.000 0.000; -0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- -1.000 0.002 -0.004 -0.000; 0.003 -0.162 -0.987 0.000; 0.003 0.987 -0.162 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTIGZ