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
>
_______________________________________________
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.
