Merge pull request #3049 from MRtrix3/voxel2mesh_fixes

voxel2mesh fixes
MRtrix3 · Feb 6, 2025 · 45d970a · 45d970a
2 parents ff2dedf + f666c76
commit 45d970a
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/cmd/voxel2mesh.cpp b/cmd/voxel2mesh.cpp
@@ -70,8 +70,10 @@ void run ()
     Surface::Algo::image2mesh_blocky (input, mesh);
 
   } else {
+
     auto input = Image<float>::open (argument[0]);
-    const default_type threshold = get_option_value ("threshold", Filter::estimate_optimal_threshold (input));
+    auto opt = get_options("threshold");
+    const default_type threshold = opt.empty() ? Filter::estimate_optimal_threshold (input) : opt[0][0];
     Surface::Algo::image2mesh_mc (input, mesh, threshold);
 
   }

diff --git a/src/surface/algo/image2mesh.h b/src/surface/algo/image2mesh.h
@@ -122,6 +122,7 @@ namespace MR
                     const auto existing = vox2vertindex.find (voxels[in_vertex]);
                     if (existing == vox2vertindex.end()) {
                       triangle_vertices[out_vertex] = vertices.size();
+                      vox2vertindex.insert(std::make_pair(voxels[in_vertex], vertices.size()));
                       Eigen::Vector3d pos_voxelspace (default_type(voxels[in_vertex][0]) - 0.5, default_type(voxels[in_vertex][1]) - 0.5, default_type(voxels[in_vertex][2]) - 0.5);
                       vertices.push_back (transform.voxel2scanner * pos_voxelspace);
                     } else {