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
> <mailto:greve@nmr.mgh.harvard.edu> <greve@nmr.mgh.harvard.edu <mailto:greve@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
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@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
> > >
> > >
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> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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MGH-NMR Center
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