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Dear list,
I have some points of interest (volume coordinates, e.g. '5.9, -27.7, 49.7') in MNI152 space. I would like to transform them to fsaverage space.
How should I do that?
I noticed that FreeSurfer comes with the file $FREESURFER_HOME/average/mni152.register.dat that contains a matrix. Is all I have to do read that matrix and apply it to each coordinate? And if so, for which direction is the matrix (do I have to invert it)?
Best,
External Email - Use Caution
Dear list,
I have some points of interest (volume coordinates, e.g. '5.9, -27.7, 49.7') in MNI152 space. I would like to transform them to fsaverage space.
How should I do that?
To answer my own question, this seems to be explained as use case #8 on the following website (at the bottom):
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
To be precise, the website explains the transformation in the opposite direction, so one should use the inverse of the matrix given on the website.
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Hi Tim,
Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is different from fsaverage: one is a volumetric space and one is a surface space.
If you are indeed looking for a transformation between MNI152 volumetric space and fsaverage surface space, you can consider the following: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registratio...
Regards, Thomas
On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear list,
I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
49.7') in MNI152 space. I would like to transform them to fsaverage space.
How should I do that?
To answer my own question, this seems to be explained as use case #8 on the following website (at the bottom):
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemsTo be precise, the website explains the transformation in the opposite direction, so one should use the inverse of the matrix given on the website.
-- Tim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Thomas,
thanks for your reply and suggestion. I had a look at the tool and its paper on it and I think it could be helpful. If I got it correctly, use case #8 at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems is referred to as 'the affine method' in the paper, but it is inferior the the non-linear warp method presented in the Wu2017_RegistrationFusion paper.
About using the github repo: The MNI152 coords I have are in a text file and they represent locations within the cortex, so I have no volume file that I want to project. But from a quick look at the repo, what I could do is to use the displacement fields (or whatever you want to call them) under bin/final_warps_FS5.3/?h.avgMapping_allSub_RF_ANTs_MNI152_orig_to_fsaverage.mat to look up the surface coords in fsaverage. Is that correct?
Thanks,
Tim
On February 11, 2019 at 1:45 AM Thomas Yeo ythomas@csail.mit.edu wrote:
External Email - Use CautionHi Tim,
Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is different from fsaverage: one is a volumetric space and one is a surface space.
If you are indeed looking for a transformation between MNI152 volumetric space and fsaverage surface space, you can consider the following: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registratio...
Regards, Thomas
On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear list,
I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
49.7') in MNI152 space. I would like to transform them to fsaverage space.
How should I do that?
To answer my own question, this seems to be explained as use case #8 on the following website (at the bottom):
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemsTo be precise, the website explains the transformation in the opposite direction, so one should use the inverse of the matrix given on the website.
-- Tim
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
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Dear Tim,
The best way to do this would be to create a volume file (e.g. each location of interest is labelled as 1), and then projecting that volume file to the fsaverage surface. For the projection step, you can use the script `CBIG_RF_projectVol2fsaverage_single.m` from `bin/scripts_final_proj` (or `CBIG_RF_projectMNI2fsaverage.m` from `bin/standalone_scripts_for_MNI_fsaverage_projection`. Make sure you choose 'nearest' interpolation if you want discrete results.
On 2/12/19, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear Thomas,
thanks for your reply and suggestion. I had a look at the tool and its paper on it and I think it could be helpful. If I got it correctly, use case #8 at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems is referred to as 'the affine method' in the paper, but it is inferior the the non-linear warp method presented in the Wu2017_RegistrationFusion paper.
About using the github repo: The MNI152 coords I have are in a text file and they represent locations within the cortex, so I have no volume file that I want to project. But from a quick look at the repo, what I could do is to use the displacement fields (or whatever you want to call them) under bin/final_warps_FS5.3/?h.avgMapping_allSub_RF_ANTs_MNI152_orig_to_fsaverage.mat to look up the surface coords in fsaverage. Is that correct?
Thanks,
Tim
On February 11, 2019 at 1:45 AM Thomas Yeo ythomas@csail.mit.edu wrote:
External Email - Use CautionHi Tim,
Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is different from fsaverage: one is a volumetric space and one is a surface space.
If you are indeed looking for a transformation between MNI152 volumetric space and fsaverage surface space, you can consider the following: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registratio...
Regards, Thomas
On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear list,
I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
49.7') in MNI152 space. I would like to transform them to fsaverage space.
How should I do that?
To answer my own question, this seems to be explained as use case #8 on the following website (at the bottom):
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemsTo be precise, the website explains the transformation in the opposite direction, so one should use the inverse of the matrix given on the website.
-- Tim
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
-- Tim
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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