When you say the content is the same, do you mean exactly the same or just the matrix? Also, what coordinate system are you trying to go to? The equation you have below takes CRS in the CT and maps it to tkrRAS in the anatomical. If you want to map the CRS in the anat then use
inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords
On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote:
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.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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