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
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