External Email - Use Caution
Hi you two,
thank you very much for your quick reply! Just two short followup questions:
@Bruce: Is this published in any paper or documentation so I can cite it?
@Doug: Has this method been implemented with the last release of FS in 6.0.0 or already before in 5.3.0 (I'm still using this version)?
Cheers Philipp
For cortical volume we compute vertex-wise volume based on dividing each obliquely truncated trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's srf2vol matlab script. On 9/6/2019 10:22 AM, Bruce Fischl wrote: Hi Philipp
I'll leave the volume question to Doug. The curvatures are estimated by fitting a second order polynomial to the local height function in the tangent bundle then computing the Hessian using the white (gray/white boundary) surface. We also have some discrete measures of curvature that uses the Gauss-Bonnet theorem, but those aren't run by default.
cheers Bruce On Fri, 6 Sep 2019, Loske, Philipp wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values.
I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search.
Best wishes
Philipp
The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.
The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
for the continuous curvature you can just cite the FreeSurfer paper, or recon1/2). For the discrete curvature I think Rudolph Pienaar published something on it. Some of the curvature indices are from David Van Essen's papers, and the volume/area calculation is Anderson M. Winkler's paper
cheers Bruce
On Mon, 9 Sep 2019, Loske, Philipp wrote:
External Email - Use Caution
Hi you two,
thank you very much for your quick reply! Just two short followup questions:
@Bruce: Is this published in any paper or documentation so I can cite it?
@Doug: Has this method been implemented with the last release of FS in 6.0.0 or already before in 5.3.0 (I'm still using this version)?
Cheers Philipp
For cortical volume we compute vertex-wise volume based on dividing each obliquely truncated trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's srf2vol matlab script.On 9/6/2019 10:22 AM, Bruce Fischl wrote: Hi Philipp
I'll leave the volume question to Doug. The curvatures are estimated by fitting a second order polynomial to the local height function in the tangent bundle then computing the Hessian using the white (gray/white boundary) surface. We also have some discrete measures of curvature that uses the Gauss-Bonnet theorem, but those aren't run by default.
cheers Bruce On Fri, 6 Sep 2019, Loske, Philipp wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values.
I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search.
Best wishes
Philipp
The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.
The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Loske, Philipp