It sounds like you are doing the right thing with the right equation. Can you elaborate on what is going wrong?
On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote: > Sorry - I meant just the matrix. > > I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I > believe. I'm a little unclear as to what exactly anat space means, but > I know that I'm trying to get it from CRS in the CT to the space in > which the surface is plotted in MATLAB, which I believe is tkrRAS, > anatomical. I'm certain it's no longer CRS space, as the x-coordinates > must contain some negative indices. > > > > On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto: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. > > > > > > > > > > _______________________________________________ > > 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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > > > > _______________________________________________ > 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
