Problems with remeshsurf and meshresample

[takfarinas medani]

Hello all

Dear Dr Fang, 

I regularly use  some functions of iso2mesh, it's a great jobs, thank you. 

But recently, I have a mesh representing the humain head with scalp, inner and outer skull layer,

attached file :myMesh_bst.dat

My code is : 

load('myMesh_bst','pnth','trih','pnti','trii','pnto','trio') %% Attached file myMesh

%% remeshsurface

[newno,newfc]=remeshsurf(pnth, trih,20);

figure('Color',[1 1 1]); %% (attached file named : scalp)

plotmesh(pnth, trih,'y>0');xlabel('X');ylabel('Y');zlabel('Z');

figure('Color',[1 1 1]); %% (attached file named : scalp_with_remeshsurf)

plotmesh(newno,newfc,'y>0');xlabel('X');ylabel('Y');zlabel('Z');

%The two figure are differentes !!

%% Assemblage des surfaces

[pnt, tri]=mergemesh(pnth,trih,pnti,trii,pnto,trio);

figure('Color',[1 1 1]);plotmesh(pnt,tri,'y>0'); % attached file named SurfMesh

xlabel('X');ylabel('Y');zlabel('Z');

legend('Scalp','InnerSkull','OuterSkull');grid;view([0 -90 0]);

%% Remplissage du volume Surface2Mesh

keepratio=1;

maxvol=1;

regions=[0 0.06019 -0.06;0 0 0.06;-0.0169 0.00035 -0.01997];

holes=[];

forcebox=1;

[node,elem,face]=surf2mesh(pnt,tri,min(pnt),max(pnt),keepratio,maxvol,regions,holes,forcebox);

figure;plotmesh(node,elem,'y>0');xlabel('X');ylabel('Y');zlabel('Z')%% 

  [no2,el2]=meshresample(node,elem,1);  % down sample the  mesh ==> ERRORS

My problems are : 

1- in %% remeshsurface

[newno,newfc]=remeshsurf(pnth, trih,20);

When I remesh the surface of the head, the obtained mesh has not the same shape! 

plotmesh(newno,newfc,'y>0'); 

give a bizare geométry (attached file named : scalp_with_remeshsurf)

I do knew why the shape of my mesh is changed? 

2- In  [node,elem,face]=surf2mesh(.....)

There is no distinction between the domaine, I specified the  regions (attached file : volumeMesh)

3- An other question: Which function is used to have a regular mesh (with the same volume of element and same density in the whole volume)

As shown in volumeMesh, I'd like to have the same mesh in all regions.

4- The function meshresample on [node,elem] doesn't work, 

the error is : Subscript indices must either be real positive integers or logicals.

I apologize for my numerous problems

Thank you advance for your help and advices

Takfarinas 

[Qianqian Fang]

On 02/03/2015 11:09 AM, takfarinas medani wrote:

...

My problems are : 

1- in %% remeshsurface

[newno,newfc]=remeshsurf(pnth, trih,20);

When I remesh the surface of the head, the obtained mesh has not the same shape! 

plotmesh(newno,newfc,'y>0'); 

give a bizare geométry (attached file named : scalp_with_remeshsurf)

I do knew why the shape of my mesh is changed?

hi Takfarinas

your opt parameter appears to be incorrect in the remeshsurf call.
when opt is a scalar, it is supposed to be the desired triangle size
after remeshing.

however, your head mesh is only 0.1962 x 0.1567 x 0.24460 unit wide
(in meters?), and you asked the resampled mesh to have a triangle size
of 20 unit! it is way too big.

if you meant to up-sample the surface, I would do the following:

ndiv=30;
dx=min(max(pnth)-min(pnth))/ndiv
[newno,newfc]=remeshsurf(pnth, trih,dx);

plotmesh(newno,newfc,'y>0');xlabel('X');ylabel('Y');zlabel('Z');

this will produce a denser surface with a target triangle size
of 0.0052 unit.

but to me, your head mesh looks fine, curious why you wanted
to remesh it?

2- In  [node,elem,face]=surf2mesh(.....)

There is no distinction between the domaine, I specified the  regions (attached file : volumeMesh)

actually, when I ran it, this call failed.

with further investigation, it was caused by using forcebox=1;

setting forcebox=1 will mesh the bounding box region outside of the
surface and the box's diagonal is specified by the p0 and p1 inputs. in your
case, you used min/max of the nodes, so the bounding box and the
inner surface intersect at the extremes.

setting forcebox=0 solved the problem. the output mesh does have
region labels (a screen shot is attached)

if you do want to add a bounding box, you need to move your p0 and
p1 away from the surface to avoid intersection.

3- An other question: Which function is used to have a regular mesh (with the same volume of element and same density in the whole volume)

As shown in volumeMesh, I'd like to have the same mesh in all regions.

if you meant to mesh all domains with roughly the same element
size (they won't be exactly the same for sure), then you should make
the maxvol parameter small enough so that the impact of the surface
node density diminishes. For example, I set maxvol to 3e-8 by

[node,elem,face]=surf2mesh(pnt,tri,min(pnt),max(pnt),1,3e-8,regions);

the plot of the output mesh is also attached.

4- The function meshresample on [node,elem] doesn't work, 

the error is : Subscript indices must either be real positive integers or logicals.

meshresample only works for surfaces, not on tetrahedral meshes.
for volumetric meshes, downsample is done by regeneration of the
mesh with larger opt.radbound and maxvol values.

I apologize for my numerous problems

Thank you advance for your help and advices

let me know if these solve your problems.

Qianqian

Takfarinas 

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[Qianqian Fang]

>> Hi Qianqian,
>> Thank you for your responses and explanation, it's very clear for me.
>> no it's work.
>> For your previous question (why I want to remesh it ) , it's
concerne an other mesh, I'd like to reduce the mesh density in order to
compare the accuracy of my results between the two models and then the
associated time consumption for the two resolutions

got you.

>> It's ok, now I understand why I have the message : intersecting
faces and regions,
>> now it's work.
>> Thank you, I get it, it's clear

>> Ok, so we cant remesh directly the volume, we need to run surf2mesh,
thank you, it's clear,

>>> I apologize for my numerous problems
>>> Thank you advance for your help and advices

no problem, I am glad it works, feel free to send in more questions :)

Qianqian