glad it worked out
Bruce
On Tue, 13 Mar 2018, Chris Adamson wrote:

So I think I have fixed it. When I swapped the volume used for geometry to 
radiological from neurological everything worked.

-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Tuesday, 13 March 2018 12:44 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

hmmm, then maybe it is something else? If you email me a surface I'll see if I 
can find time to take a look. You can also take a look at the surface normal 
calculation and see if your faces are pointing inwards. I think mris_convert -n 
will write them out

cheers
Bruce


On Mon, 12 Mar 2018, Chris Adamson
wrote:

I had already done this, it had no effect.

-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Tuesday, 13 March 2018 12:39 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Negative areas in mris_sphere, dark in
freeview

Hi Chris

we have c code for doing this but no binary that calls it in the way you need. 
This is the code:

int MRISevertSurface(MRI_SURFACE *mris) {
  int v0, fno;
  FACE *face;

  for (fno = 0; fno < mris->nfaces; fno++) {
    face = &mris->faces[fno];
    if (face->ripflag) continue;
    v0 = face->v[0];
    face->v[0] = face->v[1];
    face->v[1] = v0;
  }

  return (NO_ERROR);
}

should be easy enough to do in matlab

cheers
Bruce


On Sat, 10 Mar 2018, Chris Adamson wrote:

Hi Bruce,

Thanks for your reply. I had already tried swapping the 2nd and 3rd face 
indices, no effect.

Chris.

-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Saturday, 10 March 2018 1:06 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Negative areas in mris_sphere, dark in
freeview

Hi Chris

this probably means that the triangles aren't constructed according
to our conventions. The ordering in faces is important as the
cross-product of the legs of each triangle have to point outwards.
That's how we define the surface normal vector field. Sounds like
whatever software you used uses the oppposite convention. You could
try swapping the order of vertices in the face list

cheers
Bruce


On Fri, 9 Mar 2018, Chris Adamson wrote:


Freesurfer devs,

 

I have a baffling problem in mris_sphere.

 

I have generated some surfaces using an external tool that uses VTK.
After converting the surfaces into freesurfer format using a basic
format converter, then adding volume geometry to the surface file
using the image used to create it the surface appears dark in
freeview. When I do mris_inflate followed by mris_sphere,
mris_sphere says nearly all the triangles have negative area at the
end and it never finishes. I verified in MATLAB that the surface normals 
(computed by mris_convert) of the original white surfaces point outwards. The 
darkness in freeview is not fixed by changing the order of the indices of the 
faces (which should invert the normal). I’m at a loss to explain this.

 

Thanks in advance,

 

Chris.

 

Dr Chris Adamson

Senior Research Officer

Developmental Imaging, Clinical Sciences

 

Murdoch Childrens Research Institute

The Royal Children’s Hospital

Flemington Road, Parkville, VIC 3052 Australia

E chris.adam...@mcri.edu.au

www.mcri.edu.au

 

 

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