Hi Doug and Bruce,

So I have performed a registration outside of FreeSurfer with FLIRT that I am happy with. I had oriented both volumes in RAS first in the hope that would simplify things slightly.

The source/input/movable volume is Fake1mmMNI152_T1_0.8mm_brain.mgz The target/reference volume is RB_all_2008-03-26_means.mgz I have a FLIRT affine test.mat I want to create an lta and an xfm that reflect this affine transform

I did this:

tkregister2 --noedit --mov ../../Fake1mmMNI152_T1_0.8mm_brain.mgz --targ /usr/local/bin/freesurfer5.0/average/RB_all_2008-03-26_means.mgz --fsl ../../test.mat --ltaout ../../test.lta

But I got this error:

tkregister_tcl /usr/local/bin/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.801 -0.003 0.001 25.139; 0.000 0.822 -0.002 23.381; -0.004 0.002 0.787 10.925; 0.000 0.000 0.000 1.000; --------------------------------------- ERROR: no registration file specified

Another issue with tkregister2: setting --sd has no effect, I have to export any change I make to SUBJECTS_DIR prior to running tkregister2.

Thanks,

Matt.

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, November 07, 2011 9:28 AM To: matt@ma-tea.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Affine Matrix Conversions

Hi Matt, it is usually possible to do this with tkregister2, but not always so clear how to. Let me know if you need some directions on a specific case. doug

Matt Glasser wrote:

Hi,

I am wondering what tools FreeSurfer has to convert between different affine matrix formats.

For example, if I had a talairach.xfm that did a better job than talairach.lta, is there a way to convert from one to the other? What about FSL FLIRT matricies? Can these be interconverted with .lta?

Thanks,

Matt.

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