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 <gr...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 > 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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