Any other thoughts as to what might be going wrong with our coordinate transformations / any other transformations that we might not be taking into account?
Thanks, Isaac On Tue, Apr 29, 2014 at 4:52 PM, ISAAC PEDISICH <i...@sas.upenn.edu> wrote: > The purpose of what I'm trying to do is getting specific points from the > CT onto the average surface. > These points lie on the surface of the brain. > > Originally, we were using flirt to register the CT to the MRI, then > registering the MRI to the talairach brain, to get the CT into the same > space as the surface. This method worked okay, but we were hoping to > improve on it. > > The new method, using robust register and tkregsiter2, produces > coordinates that are on the surface of the brain in freeview, but not in > matlab (for some subjects). > > Here is the info for one problem subject: > > mri_info --vox2ras-tkr [subj]_CT_combined.img > INFO: using NIfTI-1 qform > -0.47461 0.00000 0.00000 121.50000 > 0.00000 0.00000 0.62634 -69.83636 > 0.00000 -0.47461 0.00000 121.50000 > 0.00000 0.00000 0.00000 1.00000 > > > # transform file reg_avg.lta > # created by ---- on Thu Mar 27 15:55:39 2014 > type = 1 > nxforms = 1 > mean = 256.0000 228.0000 111.0000 > sigma = 10000.0000 > 1 4 4 > 9.349995851516724e-01 -2.874486744403839e-01 -2.077235281467438e-01 > -3.043334960937500e+01 > 3.062604963779449e-01 9.497789144515991e-01 6.422379612922668e-02 > 1.133301696777344e+02 > 1.788303703069687e-01 -1.236666887998581e-01 9.760769009590149e-01 > -1.039845886230469e+02 > 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > 1.000000000000000e+00 > src volume info > valid = 1 # volume info valid > filename = [subj]_CT_combined.img > volume = 512 512 223 > voxelsize = 4.746093750000000e-01 4.746093750000000e-01 > 6.263351440429688e-01 > xras = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00 > yras = 0.000000000000000e+00 9.703245759010315e-01 2.418061196804047e-01 > zras = -0.000000000000000e+00 -2.418061196804047e-01 > 9.703245759010315e-01 > cras = 7.629394531250000e-06 -1.615307769775391e+02 1.476517486572266e+02 > dst volume info > valid = 1 # volume info valid > filename = /data/eeg/freesurfer/subjects/average/mri/orig.mgz > volume = 256 256 256 > voxelsize = 1.000000000000000e+00 1.000000000000000e+00 > 1.000000000000000e+00 > xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > yras = -2.220446049250313e-16 -1.490116119384766e-08 > -1.000000000000000e+00 > zras = 4.440892098500626e-16 1.000000000000000e+00 8.443226899772703e-18 > cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > > > Here are a set of eight coordinates, all of which are on the surface in > CRS space on the CT: > 242 267 47 > 241 283 36 > 234 298 28 > 221 313 23 > 203 321 19 > 183 323 24 > 172 312 33 > 164 297 42 > > After applying the transform, these coordinates come out as: > 5.2486 -168.8798 78.8261 > 2.2243 -174.6209 70.8729 > 2.5230 -179.4546 62.9121 > 6.0596 -183.3221 54.4805 > 12.6010 -187.6878 48.8390 > 22.2656 -187.3245 46.1419 > 29.8070 -184.1168 50.5152 > 36.3566 -180.7347 57.0374 > > Those middle coordinates are all off the brain - the coordinates are far > too negative. > > When run through the first method, they come out to: > 20.6235 -15.8172 -23.1366 > 19.041 -5.94338 -28.5567 > 20.8091 3.8041 -32.346 > 25.8047 13.9764 -34.4435 > 34.3347 20.7722 -36.4294 > 44.7823 23.7184 -33.5718 > 52.1009 18.1343 -29.1088 > 58.3186 10.0044 -24.8649 > > Which are (approximately) on the surface of the brain. > > However, when I load up the average surface in freeview, and apply > reg_avg.lta to the CT, the two overlay exactly. > > I'm mostly trying to figure out why the coordinates that I get in MATLAB > do not agree with the coordinates that I see in freeview. > > Thanks again for your help, > Isaac > > On Tue, Apr 29, 2014 at 1:43 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> 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 >> > >
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