Dear Doug,
Thanks for your quick response and suggestion. Since I put a small saline bottle on subject's left forehead, I could make sure the L-R orientation. As you suggested I just checked the images in tkregister2 without --noedit, and it seems ok. But after apply image transformation by FLIRT in FSL, I see the saline bottle on right forehead, flipped. Do you think the problem is due to FSL?
Best wishes, Yosuke
2012/5/11 Yosuke Morishima yosukemorishima@gmail.com:
Does it look flipped in tkregister2? If not, how are you judging that it is flipped? doug
Date: Fri, 11 May 2012 14:11:09 +0200 From: Yosuke Morishima yosukemorishima@gmail.com Subject: [Freesurfer] tkregister2 wrong orientation To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAOdjfTSJE818-2dTthJrJ5ii3G7wo-JDfT7oX6Kc1Q7o7XRegQ@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
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;
---- 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
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Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Institute for Empirical Research in Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email? yosukemorishima@gmail.com
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Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Institute for Empirical Research in Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email yosukemorishima@gmail.com