Dear Greve： Thank you for your reply！ I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?
2014-05-07 0:00 GMT+08:00 freesurfer-request@nmr.mgh.harvard.edu:
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Today's Topics:
- Re: Coordinate transformation to average surface space (ISAAC PEDISICH)
- Re: using multiple cores (Z K)
- Fwd: Fwd: Optseq2: ntp (Conchy PF)
- Help with subject's functional overlay (Cesar Echavarria)
- Re: Help with subject's functional overlay (Bruce Fischl)
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- Re: problems about extracting specific vertex thickness value and getting a average thickness for a specific mask (Douglas N Greve)
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- Re: Help with subject's functional overlay (Cesar Echavarria)
- Re: using multiple cores (Z K)
- Re: Help with subject's functional overlay (Douglas N Greve)
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Message: 1 Date: Mon, 5 May 2014 12:19:29 -0400 From: ISAAC PEDISICH iped@sas.upenn.edu Subject: Re: [Freesurfer] Coordinate transformation to average surface space To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: < CAPUS5aqNf_zYu185Sf723Ad9wpp59b02hC3e-K0KZ2nLjQJMdQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
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 iped@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 < greve@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 <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 sameor
just the matrix? Also, what coordinate system are you trying to goto?
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. Ihave
> freesurfer v5.3.0 installed - is there another version that Ishould
> 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 didnot
> 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:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > The matrix in the lta is probably not the right one. Tryusing
> lta_convert or tkregister2 to change it to a register.datfile
> (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 --surfpial
> --s average > > > > These steps work fine, and when I load the average brainin
> 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) byapplying:
> > > > inv(Reg_avg) * Tmov * CT_coords > > > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avgas
> > 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
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