3D Livewire

Instructions

MATLAB 7.1 or higher required

Instructions:

1. Set workspace to path that contains .hdr file
2. > view3d_lw
3. "Load from file" + filename string - Load image
   1. Enter .hdr file; or if need to switch order of slice directions...
   2. Permute instructions:
      • Permute to switch order of slice direction:
        > img = readanalyze('filename.hdr'); -- analyze -> 3d matrix
        > img = permute(a,[2 1 3]) -- switch slice #1 and #2 order
      • "Load var" + variable string - enter variable name
4. "Select slice" - Select contour on model #1 and #2 by manual livewire
   • Dots shows contour from other view
   • Up/down arrows adjust brightness, left/right arrows adjust contrast (if can't increase brightness any more, decrease contrast and increase brightness again)
   • If program stalls, click out of window and click back in
   • When done, hover around region, press space bar
5. "XZ 3D Livewire" - View progress
   • Shows rotatable 3D frame figure
   • Set marker size = 2
6. "Mask Gen" - to generate mask
7. "Output" + filename - outputs to .hdr file
8. If permuted initially, permute again
   • > writeanalyze(b,'new filename.hdr', [dimensions])... get this mm from MRIcro (x y z)
9. New LW code: use surface_points_gen.m to extract seed (surface) points into .hdr file