Dear Freesurfers,
In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make.
My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations.
Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space?
Ps: I know that the distances in spherical space are not Euclidian but still geodesic
Best wishes and thanks in advance,
Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany
Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany
Phone: +49-621-1703-6313 E-mail: christopher.milde@zi-mannheim.de Homepage: http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230
Hi Christopher
the spherical mapping usually has on the order of 17-20% distortion in distances, and the registration is probably significantly more. I'm not entirely sure what are trying to do, but you can measure the difference in great circle length between the sphere and sphere.reg to get an idea of how much additional distortion is induced by the registration
cheers Bruce
On Mon, 12 May 2014, Milde, Christopher wrote:
Dear Freesurfers,
In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make.
My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations.
Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space?
Ps: I know that the distances in spherical space are not Euclidian but still geodesic
Best wishes and thanks in advance,
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Phone: +49-621-1703-6313
E-mail: christopher.milde@zi-mannheim.de
Homepage: http://www.zi-mannheim.de/
Office: Forschungs- und Verwaltungsgebäude, Room 230
Thanx Bruce,
I will try out your suggestion and let you know. I think I will get a good estimate of the degree of metric distortions, because I have a lot of subjects tested ;-)
If this will not work, or the distortions are to big, I will make use of the Spline Tool in Freeview manually drawing a line within the cortical ribbon between the peak voxels, whereby benefitting from the reconstructed surface brain with superimposed EPI (with post inflation smoothed EPI data) for visual comparison (to benefit from the SBR versus VBR information, to avoid the problem of guessing if an activated cluster belongs to Gyrus A or B when the Cluster is spread along two attached gyri). Maybe I can also make use of the coordinate transormations RAS <-->sphere
Greetz,
Christopher
________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 12. Mai 2014 15:46 An: Freesurfer support list Betreff: Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere
Hi Christopher
the spherical mapping usually has on the order of 17-20% distortion in distances, and the registration is probably significantly more. I'm not entirely sure what are trying to do, but you can measure the difference in great circle length between the sphere and sphere.reg to get an idea of how much additional distortion is induced by the registration
cheers Bruce
On Mon, 12 May 2014, Milde, Christopher wrote:
Dear Freesurfers,
In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make.
My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations.
Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space?
Ps: I know that the distances in spherical space are not Euclidian but still geodesic
Best wishes and thanks in advance,
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Phone: +49-621-1703-6313
E-mail: christopher.milde@zi-mannheim.de
Homepage: http://www.zi-mannheim.de/
Office: Forschungs- und Verwaltungsgebäude, Room 230
Hi Christopher
I don't think you will be able to draw the geodesic distance in the ribbon in 3D as it will cut across imaging planes unpredictably. If you want the true within-subject geodesic distance there are tools for doing this (I think it was part of Mukund Balasubramanian's Ph.D. dissertation at BU among other places). Rudolph might have also implemented something like it in his tools.
cheers Bruce
On Mon, 12 May 2014, Milde, Christopher wrote:
Thanx Bruce,
I will try out your suggestion and let you know. I think I will get a good estimate of the degree of metric distortions, because I have a lot of subjects tested ;-)
If this will not work, or the distortions are to big, I will make use of the Spline Tool in Freeview manually drawing a line within the cortical ribbon between the peak voxels, whereby benefitting from the reconstructed surface brain with superimposed EPI (with post inflation smoothed EPI data) for visual comparison (to benefit from the SBR versus VBR information, to avoid the problem of guessing if an activated cluster belongs to Gyrus A or B when the Cluster is spread along two attached gyri). Maybe I can also make use of the coordinate transormations RAS <-->sphere
Greetz,
Christopher
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 12. Mai 2014 15:46 An: Freesurfer support list Betreff: Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere
Hi Christopher
the spherical mapping usually has on the order of 17-20% distortion in distances, and the registration is probably significantly more. I'm not entirely sure what are trying to do, but you can measure the difference in great circle length between the sphere and sphere.reg to get an idea of how much additional distortion is induced by the registration
cheers Bruce
On Mon, 12 May 2014, Milde, Christopher wrote:
Dear Freesurfers,
In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make.
My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations.
Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space?
Ps: I know that the distances in spherical space are not Euclidian but still geodesic
Best wishes and thanks in advance,
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Phone: +49-621-1703-6313
E-mail: christopher.milde@zi-mannheim.de
Homepage: http://www.zi-mannheim.de/
Office: Forschungs- und Verwaltungsgebäude, Room 230
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Christopher --
Indeed, you can use 'mris_pmake' to calculate the shortest distance along the surface between arbitrary mesh points.
Given a valid FreeSurfer environment, $SUBJECTS_DIR, etc:
$>mris_pmake --subj 101 --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:0,vertexEnd:10000 --mpmOverlay euclidean
will compute the shortest distance across the mesh surface itself between vertex 0 and vertex 10000 on subject '101', left hemi, smoothwm surface. Distance in mm.
HTH.
Best -=R
PS: The above syntax is for the 'dev' version of mris_pmake. Odds are that the version you might use as part of 5.3-stable is outdated. If you type something like the above and it doesn't work, let me know, and we'll put up the 'dev' version for you.
On 5/12/14, 17:17 , Bruce Fischl wrote:
Hi Christopher
I don't think you will be able to draw the geodesic distance in the ribbon in 3D as it will cut across imaging planes unpredictably. If you want the true within-subject geodesic distance there are tools for doing this (I think it was part of Mukund Balasubramanian's Ph.D. dissertation at BU among other places). Rudolph might have also implemented something like it in his tools.
cheers Bruce
On Mon, 12 May 2014, Milde, Christopher wrote:
Thanx Bruce,
I will try out your suggestion and let you know. I think I will get a good estimate of the degree of metric distortions, because I have a lot of subjects tested ;-)
If this will not work, or the distortions are to big, I will make use of the Spline Tool in Freeview manually drawing a line within the cortical ribbon between the peak voxels, whereby benefitting from the reconstructed surface brain with superimposed EPI (with post inflation smoothed EPI data) for visual comparison (to benefit from the SBR versus VBR information, to avoid the problem of guessing if an activated cluster belongs to Gyrus A or B when the Cluster is spread along two attached gyri). Maybe I can also make use of the coordinate transormations RAS <-->sphere
Greetz,
Christopher
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 12. Mai 2014 15:46 An: Freesurfer support list Betreff: Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere
Hi Christopher
the spherical mapping usually has on the order of 17-20% distortion in distances, and the registration is probably significantly more. I'm not entirely sure what are trying to do, but you can measure the difference in great circle length between the sphere and sphere.reg to get an idea of how much additional distortion is induced by the registration
cheers Bruce
On Mon, 12 May 2014, Milde, Christopher wrote:
Dear Freesurfers,
In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make.
My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations.
Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space?
Ps: I know that the distances in spherical space are not Euclidian but still geodesic
Best wishes and thanks in advance,
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany
Phone: +49-621-1703-6313
E-mail: christopher.milde@zi-mannheim.de
Homepage: http://www.zi-mannheim.de/
Office: Forschungs- und Verwaltungsgebäude, Room 230
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Milde, Christopher -
Rudolph Pienaar