Hi Doug, Thanks for the response. I'm not seeing lta_convert as an executable that I can run. I have freesurfer v5.3.0 installed - is there another version that I should be using?
For using tkregister2, I'm a bit confused as to what I should be doing. I had assumed (erroneously, it seems) that the .lta and .dat files contained the same information. I just tried re-running tkregister2 with the command: tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s average --lta reg_avg.lta Such that I can pass in the reg_avg.lta file created from robust register, and have it output a reg_avg.dat file. The contents of these two files, however, seem to be exactly the same.
I also running tkregister2 with the --fslregout and --freeview flags, but neither of those produced a correct transformation either.
Martin: We are indeed registering the CT to an average MRI, and for the moment we are correcting inaccuracies manually with tkregister2. I just tried bbregister with one of our problem subjects, and it still produced a matrix that had to be significantly adjusted in tkregister2. Furthermore, the matrix that it produced still did not transform the coordinates correctly in MATLAB.
-Isaac
On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug
On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
Hi All,
I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject.
By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should.
However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying:
inv(Reg_avg) * Tmov * CT_coords
with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended).
As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this?
Thanks, Isaac
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