Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
Bruce,
and do you require that also all volumes which are passed as arguments to mris_make_surfaces must have identical vox2ras and also the vox2ras of the volumes has to be identical to vox2ras of all surfaces?
And, still it is not clear to me this:
In freeview, there is perfect overlap of ?h.white.deformed and lh.white, but for the selected vertex the freeview shows different coordinates in lh.white and lh.white.defomed (see screenshot, note the perfect overlap of the meshes). My click on the surface in 3D view mode selects vertex no 66639 in both surfaces, located at the same position on the screen, however the vertex coordinates shown in freeview are different.
How it is possible?
Antonin
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonin Skoch ansk@ikem.cz Sent: 11/23/2016 2:26 AM Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
no, they look fine in freeview because freeview is treating them as sseparate surfaces. In mris_make_surfaces we are assuming it is the same surface (same ras2vox, same number of vertices/faces, etc...)
On Wed, 23 Nov 2016, Antonin Skoch wrote:
Dear Bruce,
I am trying to understand. The vox2ras are indeed different:
lh.white
Volume Geometry vox2ras -0.70000 0.00000 0.00000 108.35732; 0.00000 0.00000 0.70000 -131.16824; 0.00000 -0.70000 0.00000 112.74670; 0.00000 0.00000 0.00000 1.00000;
lh.white.deformed
Volume Geometry vox2ras -0.70000 0.00000 0.00000 108.33944; 0.00000 0.00000 0.70000 -127.46620; 0.00000 -0.70000 0.00000 109.73940; 0.00000 0.00000 0.00000 1.00000;
But when I load both surfaces in freeview, they perfectly fit, optically there is perfect vertex-by vertex match (by looking at the mesh rendering or 2D surface contour, even with extended zoom). However, vertices show different RAS coordinates in freeview cursor display, for example vertex 136135 in lh.white.deformed shows coords -1.36 -6.9 21.69, in lh.white shows coords -1.38 -3.2 18.68.
It is some kind of issue of freeview?
Antonin
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonin Skoch ansk@ikem.cz Cc: freesurfer@nmr.mgh.harvard.edu Sent: 11/23/2016 1:43 AM Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
the vox2ras. Not sure about the HCP pipeline. They use a deprecated version of FS, but in any case what you had would not work as the ?h.pial surface didn't match the ?h.white.deformed one. If you also deformed the pial it would be ok
On Wed, 23 Nov 2016, Antonin Skoch wrote:
> Dear Bruce, > > thank you very much for your time. > > Concerning transformations, that is weird since I adopted my code from HCP pipelines > >https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/sc...
> rferHiresPial.sh > > and there I think they use the surfaces precisely this way. They are using the surfaces > generated by 1mm3 volumes as input and refine them by using co-registered higher > resolution volumes. I use full-hires reconstruction, but for my safety and convenience I > left the code with transformations, which (I thought) should do not any harm (there is > not any resampling in my case). > > I also checked the white and white.deformed processed by default HCP pipeline and they do > NOT have the same ras2vox. > > BTW, which transformation in mris_info is relevant for this case? I found several of them > in mris_info: > > talairch.xfm > > surfaceRAS to talaraiched surfaceRAS > > talairached surfaceRAS to surfaceRAS > > Volume Geometry vox2ras > > Volume Geometry vox2ras-tkr > > Antonin > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > To: Antonin Skoch ansk@ikem.cz > Sent: 11/23/2016 12:42 AM > Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with > overlapping pial surfaces > > yes, and I tracked it down and fixed it. BTW: don't use the > white.deformed surface - use the white one. You can't use one surface that > has been transformed (i.e. has a different ras2vox) and other surfaces that > have not (you can see this if you run mris_info on the surface files, the > ras2vox should match in all of them) > > cheers > Bruce > > > >
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yes, all the surfaces used by mris_make_surface must share things like ras2vox and such
cheers and happy thanksgiving Brue On Wed, 23 Nov 2016, Antonin Skoch wrote:
Bruce,
and do you require that also all volumes which are passed as arguments to mris_make_surfaces must have identical vox2ras and also the vox2ras of the volumes has to be identical to vox2ras of all surfaces?
And, still it is not clear to me this:
In freeview, there is perfect overlap of ?h.white.deformed and lh.white, but for the selected vertex the freeview shows different coordinates in lh.white and lh.white.defomed (see screenshot, note the perfect overlap of the meshes). My click on the surface in 3D view mode selects vertex no 66639 in both surfaces, located at the same position on the screen, however the vertex coordinates shown in freeview are different.
How it is possible?
Antonin
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonin Skoch ansk@ikem.cz Sent: 11/23/2016 2:26 AM Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
no, they look fine in freeview because freeview is treating them as sseparate surfaces. In mris_make_surfaces we are assuming it is the same surface (same ras2vox, same number of vertices/faces, etc...) On Wed, 23 Nov 2016, Antonin Skoch wrote: > Dear Bruce, > > I am trying to understand. The vox2ras are indeed different: > > lh.white > > Volume Geometry vox2ras > -0.70000 0.00000 0.00000 108.35732; > 0.00000 0.00000 0.70000 -131.16824; > 0.00000 -0.70000 0.00000 112.74670; > 0.00000 0.00000 0.00000 1.00000; > > lh.white.deformed > > Volume Geometry vox2ras > -0.70000 0.00000 0.00000 108.33944; > 0.00000 0.00000 0.70000 -127.46620; > 0.00000 -0.70000 0.00000 109.73940; > 0.00000 0.00000 0.00000 1.00000; > > But when I load both surfaces in freeview, they perfectly fit, optically there is perfect > vertex-by vertex match (by looking at the mesh rendering or 2D surface contour, even with > extended zoom). > However, vertices show different RAS coordinates in freeview cursor display, for example > vertex 136135 in lh.white.deformed shows coords -1.36 -6.9 21.69, in lh.white shows > coords -1.38 -3.2 18.68. > > It is some kind of issue of freeview? > > Antonin > > > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> > To: Antonin Skoch <ansk@ikem.cz> > Cc: <freesurfer@nmr.mgh.harvard.edu> > Sent: 11/23/2016 1:43 AM > Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with > overlapping pial surfaces > > the vox2ras. Not sure about the HCP pipeline. They use a deprecated > version of FS, but in any case what you had would not work as the ?h.pial > surface didn't match the ?h.white.deformed one. If you also deformed > the pial it would be ok > > On Wed, 23 Nov 2016, Antonin > Skoch wrote: > > > Dear Bruce, > > > > thank you very much for your time. > > > > Concerning transformations, that is weird since I adopted my code from HCP > pipelines > > > >https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/scri pts/FreeSu > > > rferHiresPial.sh > > > > and there I think they use the surfaces precisely this way. They are using > the surfaces > > generated by 1mm3 volumes as input and refine them by using co-registered > higher > > resolution volumes. I use full-hires reconstruction, but for my safety and > convenience I > > left the code with transformations, which (I thought) should do not any > harm (there is > > not any resampling in my case). > > > > I also checked the white and white.deformed processed by default HCP > pipeline and they do > > NOT have the same ras2vox. > > > > BTW, which transformation in mris_info is relevant for this case? I found > several of them > > in mris_info: > > > > talairch.xfm > > > > surfaceRAS to talaraiched surfaceRAS > > > > talairached surfaceRAS to surfaceRAS > > > > Volume Geometry vox2ras > > > > Volume Geometry vox2ras-tkr > > > > Antonin > > > > > > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> > > To: Antonin Skoch <ansk@ikem.cz> > > Sent: 11/23/2016 12:42 AM > > Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement > -issue with > > overlapping pial surfaces > > > > yes, and I tracked it down and fixed it. BTW: don't use the > > white.deformed surface - use the white one. You can't use one surface > that > > has been transformed (i.e. has a different ras2vox) and other > surfaces that > > have not (you can see this if you run mris_info on the surface files, > the > > ras2vox should match in all of them) > > > > cheers > > Bruce > > > > > > > > > > > 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. > > >
Dear Bruce,
I understand the requirement about surfaces. But what about the volumes passed to mris_make_surfaces, do they have the same vox2ras as the surfaces?
Maybe it could be a good option to incorporate checks of this to mris_make_surfaces binary to prevent possible problems caused by this.
Regards,
Antonin
yes, all the surfaces used by mris_make_surface must share things like ras2vox and such
cheers and happy thanksgiving Brue On Wed, 23 Nov 2016, Antonin Skoch wrote:
Bruce,
and do you require that also all volumes which are passed as arguments to mris_make_surfaces must have identical vox2ras and also the vox2ras of the volumes has to be identical to vox2ras of all surfaces?
And, still it is not clear to me this:
In freeview, there is perfect overlap of ?h.white.deformed and lh.white, but for the selected vertex the freeview shows different coordinates in lh.white and lh.white.defomed (see screenshot, note the perfect overlap of the meshes). My click on the surface in 3D view mode selects vertex no 66639 in both surfaces, located at the same position on the screen, however the vertex coordinates shown in freeview are different.
How it is possible?
Antonin
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonin Skoch ansk@ikem.cz Sent: 11/23/2016 2:26 AM Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
no, they look fine in freeview because freeview is treating them as sseparate surfaces. In mris_make_surfaces we are assuming it is the same surface (same ras2vox, same number of vertices/faces, etc...)
On Wed, 23 Nov 2016, Antonin Skoch wrote:
> Dear Bruce, > > I am trying to understand. The vox2ras are indeed different: > > lh.white > > Volume Geometry vox2ras > -0.70000 0.00000 0.00000 108.35732; > 0.00000 0.00000 0.70000 -131.16824; > 0.00000 -0.70000 0.00000 112.74670; > 0.00000 0.00000 0.00000 1.00000; > > lh.white.deformed > > Volume Geometry vox2ras > -0.70000 0.00000 0.00000 108.33944; > 0.00000 0.00000 0.70000 -127.46620; > 0.00000 -0.70000 0.00000 109.73940; > 0.00000 0.00000 0.00000 1.00000; > > But when I load both surfaces in freeview, they perfectly fit, optically there is perfect > vertex-by vertex match (by looking at the mesh rendering or 2D surface contour, even with > extended zoom). > However, vertices show different RAS coordinates in freeview cursor display, for example > vertex 136135 in lh.white.deformed shows coords -1.36 -6.9 21.69, in lh.white shows > coords -1.38 -3.2 18.68. > > It is some kind of issue of freeview? > > Antonin > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > To: Antonin Skoch ansk@ikem.cz > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: 11/23/2016 1:43 AM > Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with > overlapping pial surfaces > > the vox2ras. Not sure about the HCP pipeline. They use a deprecated > version of FS, but in any case what you had would not work as the ?h.pial > surface didn't match the ?h.white.deformed one. If you also deformed > the pial it would be ok > > On Wed, 23 Nov 2016, Antonin > Skoch wrote: > > > Dear Bruce, > > > > thank you very much for your time. > > > > Concerning transformations, that is weird since I adopted my code from HCP > pipelines > > > >https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/sc... pts/FreeSu > > > rferHiresPial.sh > > > > and there I think they use the surfaces precisely this way. They are using > the surfaces > > generated by 1mm3 volumes as input and refine them by using co-registered > higher > > resolution volumes. I use full-hires reconstruction, but for my safety and > convenience I > > left the code with transformations, which (I thought) should do not any > harm (there is > > not any resampling in my case). > > > > I also checked the white and white.deformed processed by default HCP > pipeline and they do > > NOT have the same ras2vox. > > > > BTW, which transformation in mris_info is relevant for this case? I found > several of them > > in mris_info: > > > > talairch.xfm > > > > surfaceRAS to talaraiched surfaceRAS > > > > talairached surfaceRAS to surfaceRAS > > > > Volume Geometry vox2ras > > > > Volume Geometry vox2ras-tkr > > > > Antonin > > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > To: Antonin Skoch ansk@ikem.cz > > Sent: 11/23/2016 12:42 AM > > Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement > -issue with > > overlapping pial surfaces > > > > yes, and I tracked it down and fixed it. BTW: don't use the > > white.deformed surface - use the white one. You can't use one surface > that > > has been transformed (i.e. has a different ras2vox) and other > surfaces that > > have not (you can see this if you run mris_info on the surface files, > the > > ras2vox should match in all of them) > > > > cheers > > Bruce > > > > > > > > > > > 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
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Antonin Skoch -
Bruce Fischl