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Hi Freesurfer team,
Sorry to ask a new question about FreeSurfer coordinates (I know it has been debated multiple times reading old messages) but I am still confused with all these spaces. I have a very simple use case in Freeview, when I load the T1.mgz image I would need to get the "TkReg RAS" coordinate of points using the pixel positions (last line in Cursor/Mouse coordinates in Freeview). I know Freeview is providing the conversion but I would need to be able to extract the "TkReg RAS" coordinates for multiple pixel positions in the T1.mgz file.
I've read the FreeSurfer documentation (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but it is still confused for me when I look at the coordinates in Freeview... Which transformation is used to convert pixel coordinate (T1.mgz) to Talairach, TKReg RAS and RAS systems? I also found this interesting link http://brainmap.org/icbm2tal/ and implemented the mni2tal / spm2tal / fsl2tal / other2tal transformations (in Python/Numpy) but unfortunately none of them gave me good results.
Thanks for your help.
Florent
Hi Florent
if you run mris_info on the surface of interest it will print out the vox2ras-tkr matrix that you can use for this conversion.
cheers Bruce
On Fri, 26 Oct 2018, k3ops@free.fr wrote:
External Email - Use CautionHi Freesurfer team,
Sorry to ask a new question about FreeSurfer coordinates (I know it has been debated multiple times reading old messages) but I am still confused with all these spaces. I have a very simple use case in Freeview, when I load the T1.mgz image I would need to get the "TkReg RAS" coordinate of points using the pixel positions (last line in Cursor/Mouse coordinates in Freeview). I know Freeview is providing the conversion but I would need to be able to extract the "TkReg RAS" coordinates for multiple pixel positions in the T1.mgz file.
I've read the FreeSurfer documentation (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but it is still confused for me when I look at the coordinates in Freeview... Which transformation is used to convert pixel coordinate (T1.mgz) to Talairach, TKReg RAS and RAS systems? I also found this interesting link http://brainmap.org/icbm2tal/ and implemented the mni2tal / spm2tal / fsl2tal / other2tal transformations (in Python/Numpy) but unfortunately none of them gave me good results.
Thanks for your help.
Florent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Florent,
I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get
-24, -55, 62
Which matches what is shown in freeview.
Best, Ruopeng
On 10/26/2018 12:06 PM, k3ops@free.fr wrote:
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Hi Bruce,
Thanks for the tip. When I run the command on 'lh.white' surface for example, I don't get an affine transform but a simpler one:
vox2ras-tk: -1 0 0 128 0 0 1 -128 0 -1 0 128 0 0 0 1
So when I apply this transform to a pixel position (152, 66, 73) here is the result I get: -152, 73, -66
But the expected result provided in Freeview as TkRegRAS T1 is: -23.61, -55.02, 61.25
Which obviously involving an affine transform.
Did I miss something? Thanks
Cheers, Florent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Ruopen and Bruce,
indeed I fixed the transform multiplication and now I am able to get the good coordinates. Thanks for your help!
Best, Florent
----- Mail original ----- De: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu À: freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 26 Octobre 2018 19:08:28 Objet: Re: [Freesurfer] Freeview coordinates
Hi Florent,
I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get
-24, -55, 62
Which matches what is shown in freeview.
Best, Ruopeng
On 10/26/2018 12:06 PM, k3ops@free.fr wrote:
External Email - Use Caution Hi Bruce,
Thanks for the tip. When I run the command on 'lh.white' surface for example, I don't get an affine transform but a simpler one:
vox2ras-tk: -1 0 0 128 0 0 1 -128 0 -1 0 128 0 0 0 1
So when I apply this transform to a pixel position (152, 66, 73) here is the result I get: -152, 73, -66
But the expected result provided in Freeview as TkRegRAS T1 is: -23.61, -55.02, 61.25
Which obviously involving an affine transform.
Did I miss something? Thanks
Cheers, Florent
_______________________________________________ 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
glad to hear it Bruce On Mon, 29 Oct 2018, k3ops@free.fr wrote:
External Email - Use CautionHi Ruopen and Bruce,
indeed I fixed the transform multiplication and now I am able to get the good coordinates. Thanks for your help!
Best, Florent
----- Mail original ----- De: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu À: freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 26 Octobre 2018 19:08:28 Objet: Re: [Freesurfer] Freeview coordinates
Hi Florent,
I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get
-24, -55, 62
Which matches what is shown in freeview.
Best, Ruopeng
On 10/26/2018 12:06 PM, k3ops@free.fr wrote:
External Email - Use Caution Hi Bruce,
Thanks for the tip. When I run the command on 'lh.white' surface for example, I don't get an affine transform but a simpler one:
vox2ras-tk: -1 0 0 128 0 0 1 -128 0 -1 0 128 0 0 0 1
So when I apply this transform to a pixel position (152, 66, 73) here is the result I get: -152, 73, -66
But the expected result provided in Freeview as TkRegRAS T1 is: -23.61, -55.02, 61.25
Which obviously involving an affine transform.
Did I miss something? Thanks
Cheers, Florent
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
k3ops＠free.fr -
Ruopeng Wang