You should run tkregister2 without the --noedit to see if your registration is correct. When you use --regheader, it will compute the registration based on the scanner cooridinates in the mgz files. They apparently have the same coordinates because the matrix is the identity

On 10/17/16 11:47 AM, Chiara Giacosa wrote:

Dear experts,

I am new to freesurfer and I am struggling making transformation of images from one subject to another as well as to a template. I have tried different ways, but I always end up with the original image as if the transformation was never applied. I used tkregister2 from command line and mri_vol2vol.

I noticed that the transformation matrices are always the identity matrix in the first 3 columns/rows, no matter what transformation I tell the program to do. I don't think that this makes sense so I wonder if I am doing something wrong or if there might be an issue with the version of tkregister I have.

My commands are:

tkregister2 --mov $subj/mri/orig.mgz --targ my_template/mri/orig.mgz --regheader --reg $subj/reg/orig2templ_tkreg.dat --noedit

mri_vol2vol --mov $subj/mri/rh.hand_manual.nii.gz --targ my_template/mri/orig.mgz --o $subj/mri/rh.hand_subj_in_mytempl.mgz --reg $subj/reg/orig2templ_tkreg.dat

Output Matrix $subj/reg/orig2templ_tkreg.da:

subject-unknown

1.000000

1.000000

0.150000

1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.370635986328125e+00

0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 -4.750839233398438e+00

0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -1.000000000000000e+00

0 0 0 1

round

Contents of my $FREESURFER_HOME/build-stamp.txt file:

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Any suggestion will be much appreciated!

--

Chiara Giacosa
Ph.D. candidate
Concordia University
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