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!