Hi Patricia
I’m not sure why there are differences in your distribution, but it is a different processing that generates the intermediate surfaces. It is not driven by image intensities at all Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Patricia Pais Roldan Sent: Tuesday, June 23, 2020 12:57 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mesh spatial resolution after mris_expand
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Hi Bruce,
thanks for your comment. Indeed, as you expected, my pial faces are bigger than my white faces, but my problem is with the surfaces generated by mris_expand. To summarize:
- I'm generating 4 surfaces between white and pial.
- If we focus for example in vertices located in gyri, the distances between the vertices tend to get bigger in surfaces generated closer to the pial boundary.
So far everything makes sense.
- However, when I plot the distribution of the distance between vertices for the white, pial and intermediate surfaces, I see that there is a change in the left part of the distribution ONLY FOR THE INTERMEDIATE SURFACES, which I cannot explain unless there's something going on with the function mris_expand that I used to generate the intermediate surfaces. See the image below:
[cid:image001.jpg@01D64A21.48CF2700]
Red= Distribution of the distance between vertices of cortical gyri; Blue= distribution of the distance between vertices of cortical sulci. Note the left tail is "pushed" towards the right in the intermediate surfaces (layer02 -- layer08).
This probably affects only a set of vertices which are not representative, but I'm still wondering why it happens.
Thank you very much again.
Cheers
On 22.06.20 16:28, Fischl, Bruce wrote: Hi Patricia
mris_info will give you some stats on vertex spacing, face area, etc…. I expect the pial faces will be a bit bigger/farther apart since it contains a greater volume.
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Patricia Pais Roldan Sent: Monday, June 22, 2020 12:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mesh spatial resolution after mris_expand
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Dear freesurfer community,
I'd like to know if there's any difference between the characteristics of a white or pial surface generated during the standard recon-all and a surface generated through mris_expand (e.g. mris_expand -thickness lh.white 0.2 lh.whitePlus02). In my results, it seems that in some areas the vertices of mris_expand-generated surfaces are more separated from each other (i.e., larger triangles or lower resolution -see original question for details-).
Thank you very much.
Patricia
On 04.05.20 09:20, Patricia Pais wrote:
Dear FreeSurfer developers,
I'm generating white and pial surfaces using recon-all on an MP2RAGE to later create intermediate surfaces using mris_expand (for example: mris_expand -thickness lh.white_smooth 0.2 lh.layer02, with lh.white_smooth being a smoothed version of lh.white).
It all looked fine until I decided to calculate the vertex-to-vertex distance and plotted the distribution of this parameter (something like the "spatial resolution of the mesh") for all the generated surfaces.
In the histograms below, you see "distance between vertices" on the X axis and "number of samples" (pairs of vertices) on the Y axis (left/right plots: left/right hemisphere, blue=sulci vertices, red=gyri vertices).
The distributions are in agreement with previously published work, but I see a small peak on the left (around 0.25 mm) in intermediate surfaces, like an accumulation of points with a certain vertex-to-vertex distance instead of a gradual decrease towards 0 (pial and white are ok).
I traced back the points in these bumps and I confirmed that those vertices in intermediate surfaces correspond to vertices on the left tail of the curve in the pial and white surfaces, so I'm not very worried about it, but I'd like to know whether there's some kind of minimum distance between the vertices of the surfaces generated by mris_expand or any other reason that can explain my results.
Thank you very much in advance!
[cid:image002.png@01D64A21.48CF2700]
Best regards,
Patricia
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