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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.adamson@mcri.edu.au
www.mcri.edu.au
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