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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