mrisurf, mris_convert #NF. Added function to copy coords from one sur…

…face to another (good for patches). Added function to mris_convert with --to-surf
ayendiki · Apr 16, 2021 · b1d3b65 · b1d3b65
1 parent fe0ae16
commit b1d3b65
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Showing 3 changed files with 46 additions and 0 deletions.
diff --git a/include/mrisurf.h b/include/mrisurf.h
@@ -2464,6 +2464,7 @@ static bool mrisVerticesAreNeighbors(MRIS const * const mris, int const vno1, in
 int MRISripMidline(MRI_SURFACE *mris, MRI *mri_aseg, MRI *mri_brain, const char *hemi, int which, int fix_mtl);
 int MRIcomputeLabelNormal(MRI *mri_aseg, int x0, int y0, int z0,int label, int whalf, double *pnx, double *pny,
 			  double *pnz, int use_abs);
+int MRIScopyCoords(MRIS *surf, MRIS *surfcoords);
 int MRISfindExpansionRegions(MRI_SURFACE *mris);
 int MRISwriteField(MRIS *surf, const char **fields, int nfields, const char *outname);
 

diff --git a/mris_convert/mris_convert.cpp b/mris_convert/mris_convert.cpp
@@ -124,6 +124,8 @@ static int cras_add = 0;
 static int cras_subtract = 0;
 static int ToScanner = 0;
 static int ToTkr = 0;
+static int ToSurfCoords = 0;
+MRIS *SurfCoords = NULL;
 int WriteArea = 0;
 
 int DeleteCommands = 0;
@@ -323,6 +325,11 @@ main(int argc, char *argv[])
     printf("Subtracting scanner CRAS from surface xyz\n");
     MRISshiftCRAS(mris, -1);
   }
+  if(ToSurfCoords){
+    printf("Converting to coords of --to-surf surface\n");
+    int err = MRIScopyCoords(mris,SurfCoords);
+    if(err) exit(1);
+  }
   if(ToScanner){
     printf("Converting from tkr to scanner coordinates\n");
     MRIStkr2Scanner(mris);
@@ -797,6 +804,12 @@ get_option(int argc, char *argv[])
     cras_add = 0;
     cras_subtract = 0;
   }
+  else if (!stricmp(option, "-to-surf")) {
+    ToSurfCoords = 1;
+    SurfCoords = MRISread(argv[2]);
+    if(SurfCoords == NULL) exit (1);
+    nargs = 1 ;
+  }
   else if (!stricmp(option, "-vol-geom"))
   {
     VolGeomMRI = MRIreadHeader(argv[2],MRI_VOLUME_TYPE_UNKNOWN);
@@ -921,6 +934,7 @@ print_help(void)
   printf( "  --userealras : set the useRealRAS flag in the surface file to 1 \n") ;
   printf( "  --usesurfras : set the useRealRAS flag in the surface file to 0 \n") ;
   printf( "  --vol-geom MRIVol : use MRIVol to set the volume geometry\n") ;
+  printf( "  --to-surf surfcoords : copy coordinates from surfcoords to output (good for patches)\n") ;
   printf( "  --to-scanner : convert coordinates from native FS (tkr) coords to scanner coords\n") ;
   printf( "  --to-tkr : convert coordinates from scanner coords to native FS (tkr) coords \n") ;
   printf( "  --volume ?h.white ?h.pial ?h.volume : compute vertex-wise volume, no other args needed (uses th3)\n") ;

diff --git a/utils/mrisurf.cpp b/utils/mrisurf.cpp
@@ -879,3 +879,34 @@ int MRIcomputeLabelNormal(MRI *mri_aseg, int x0, int y0, int z0,
   *pnz = nz ;
   return(NO_ERROR) ;
 }
+
+/*!
+  \fn int MRIScopyCoords(MRIS *surf, MRIS *surfcoords)
+  \brief Transfers the xyz coords from surfcoords to the given surface.
+*/
+int MRIScopyCoords(MRIS *surf, MRIS *surfcoords)
+{
+  int k;
+
+  if(surf == NULL){
+    printf("ERROR: MRIScopyCoordsCoords(): surf is null\n");
+    return(1);
+  }
+  if(surfcoords == NULL){
+    printf("ERROR: MRIScopyCoordsCoords(): surfcoords is null\n");
+    return(1);
+  }
+  if(surf->nvertices != surfcoords->nvertices){
+    printf("ERROR: MRIScopyCoordsCoords(): surf and surfcoords have diff no of vetices\n");
+    return(1);
+  }
+
+  for(k=0; k < surf->nvertices; k++){
+    VERTEX *v = &surf->vertices[k];
+    //if(v->ripflag) continue;
+    v->x = surfcoords->vertices[k].x;
+    v->y = surfcoords->vertices[k].y;
+    v->z = surfcoords->vertices[k].z;
+  }
+  return(0);
+}