Thanks very much, Bruce. That saves me a ton of effort. Let me confirm a few key details. The command with -n kicks out a file with 2 header lines, a list of normals, and a list of triangles for which each is defined by its 3 vertex numbers. I see the format for a "Triangle Surface File - ASCII version" on Graham Wideman's web pages created many moons ago: http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm#TriangleASCII
Can you point me to more up-to-date and detailed info, perhaps on the wiki? (1) Are the normals in TkRAS coordinates? I can check this pretty easily. Please pardon my laziness in asking. (2) The list of normals I presume are in order beginning at vertex number zero?? I would like to make sure I identify the correct vertex number for each normal. How? (3) Are the normals consistently pointing one way, e.g. ctx --> wm? (4) Is the order of the vertex numbers for each triangle consistent to provide reliable ctx --> wm directionality. If so is it (v1-v2)X(v2-v3) or vica versa? Best regards, Don > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, October 13, 2015 8:45 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] list of normals to triangle vertices > > Hi Don > > mris_convert -n lh.white lh.white.normals.asc > > should do the trick. And this is the way that the area is computed (from > mrisurf.c): > > static float > mrisTriangleArea(MRIS *mris, int fac, int n) { > int n0,n1; > face_type *f; > float v0[3],v1[3],d1,d2,d3; > > n0 = (n == 0) ? VERTICES_PER_FACE-1 : n-1; > n1 = (n == VERTICES_PER_FACE-1) ? 0 : n+1; > f = &mris->faces[fac]; > v0[0] = mris->vertices[f->v[n]].x - mris->vertices[f->v[n0]].x; > v0[1] = mris->vertices[f->v[n]].y - mris->vertices[f->v[n0]].y; > v0[2] = mris->vertices[f->v[n]].z - mris->vertices[f->v[n0]].z; > v1[0] = mris->vertices[f->v[n1]].x - mris->vertices[f->v[n]].x; > v1[1] = mris->vertices[f->v[n1]].y - mris->vertices[f->v[n]].y; > v1[2] = mris->vertices[f->v[n1]].z - mris->vertices[f->v[n]].z; > d1 = -v1[1]*v0[2] + v0[1]*v1[2]; > d2 = v1[0]*v0[2] - v0[0]*v1[2]; > d3 = -v1[0]*v0[1] + v0[0]*v1[1]; > return sqrt(d1*d1+d2*d2+d3*d3)/2; > } > > > > cheers > Bruce > > > On Tue, 13 Oct 2015, Krieger, Donald N. wrote: > > > > > Hi everyone, > > > > > > > > I need to create the vector normal to the surface at each “white” vertex. > > > > I would like to end up with 7 fields in each entry: > > > > 1 Vertex number > > > > 2-4 RAS coordinates > > > > 5-7 RAS components of the normal vector pointed from ctx à wm > > > > > > > > mri_annotation2label gets me the first 4. > > > > I just don’t want to reinvent the wheel getting the normal. > > > > If there’s a way to get freesurfer to kick out the normals, that would > > be best. > > > > Here are naïve questions that arise out of this problem: > > > > 1. Is there a simple way to identify which vertices are “nearest > > neighbors” other than measuring and sorting the distances between each > > and all the others i.e. which ones form a triangle? I understand to > > use the normalized average of the 6 triangles which include the vertex. > > > > 2. Is there a simple way to identify the order of the sides of > > each triangle so that their cross product is ordered correctly to > > produce ctx à wm? > > > > > > > > Thanks for your help with this. > > > > > > > > Don > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
