Difference between revisions of "Medical Imaging Example Meshes"

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Line 29: Line 29:
  
 
Generated mesh with delta = 2, [https://odu.box.com/s/7kgv263qvebk55077nny4l2n7ienpahf Output Mesh]
 
Generated mesh with delta = 2, [https://odu.box.com/s/7kgv263qvebk55077nny4l2n7ienpahf Output Mesh]
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<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Head-Neck.mha --delta 2 --output ./Head-Neck,d=2.vtk</pre>
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<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Head-Neck.mha --delta 2 --output ./Head-Neck,d=2.vtk</pre>
  
 
[[File:Head-Neck,d=2.png|500px|Head-Neck,d=2.png]]
 
[[File:Head-Neck,d=2.png|500px|Head-Neck,d=2.png]]
  
 
Generated mesh with delta = 1.5, [https://odu.box.com/s/sfjb83whac8rhn1ykuuxmektprxtci78 Output Mesh]
 
Generated mesh with delta = 1.5, [https://odu.box.com/s/sfjb83whac8rhn1ykuuxmektprxtci78 Output Mesh]
−
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk</pre>
+
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk</pre>
  
 
[[File:Head-Neck,d=1.5.png|500px|Head-Neck,d=1.5.png]]
 
[[File:Head-Neck,d=1.5.png|500px|Head-Neck,d=1.5.png]]
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Generated mesh with delta = 1,5, [https://odu.box.com/s/wfeqw6c65si0kync8yi20cychyqxmpcs Output Mesh]
 
Generated mesh with delta = 1,5, [https://odu.box.com/s/wfeqw6c65si0kync8yi20cychyqxmpcs Output Mesh]
−
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Brain-With-Tumor-Case17.nii --delta 1.5 --output ./Brain-With-Tumor-Case17,d=1.5.vtk</pre>
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<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Brain-With-Tumor-Case17.nii --delta 1.5 --output ./Brain-With-Tumor-Case17,d=1.5.vtk</pre>
  
 
[[File:Brain-With-Tumor-Case17,d=1.5.png|500px|Brain-With-Tumor-Case17,d=1.5.png]]
 
[[File:Brain-With-Tumor-Case17,d=1.5.png|500px|Brain-With-Tumor-Case17,d=1.5.png]]
  
 
Generated mesh with delta = 1.5 and volume-grading, [https://odu.box.com/s/83pl6vgzabzclsbqyzujmtqjbfckil2s Output Mesh]
 
Generated mesh with delta = 1.5 and volume-grading, [https://odu.box.com/s/83pl6vgzabzclsbqyzujmtqjbfckil2s Output Mesh]
−
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Brain-With-Tumor-Case17.nii --delta 1.5 --volume-grading --output ./Brain-With-Tumor-Case17,d=1.5,grading.vtk</pre>
+
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Brain-With-Tumor-Case17.nii --delta 1.5 --volume-grading --output ./Brain-With-Tumor-Case17,d=1.5,grading.vtk</pre>
  
 
[[File:Brain-With-Tumor-Case17,d=1.5,grading.png|500px|Brain-With-Tumor-Case17,d=1.5,grading.png]]
 
[[File:Brain-With-Tumor-Case17,d=1.5,grading.png|500px|Brain-With-Tumor-Case17,d=1.5,grading.png]]
Line 55: Line 55:
  
 
Generated mesh with delta = 1,5, [https://odu.box.com/s/udhiz0u5bewtqi9z07owiejno9gjzb1j Output Mesh]
 
Generated mesh with delta = 1,5, [https://odu.box.com/s/udhiz0u5bewtqi9z07owiejno9gjzb1j Output Mesh]
−
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Knee-Char.mha --delta 1.5 --output ./Knee-Char,d=1.5.vtk</pre>
+
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Knee-Char.mha --delta 1.5 --output ./Knee-Char,d=1.5.vtk</pre>
  
 
[[File:Knee-Char,d=1.5.png|500px|Knee-Char,d=1.5.png]]
 
[[File:Knee-Char,d=1.5.png|500px|Knee-Char,d=1.5.png]]
  
 
Generated mesh with delta = 1.5 and volume-grading, [https://odu.box.com/s/tmmv1kjb925zclnshegypovxmaxablcs Output Mesh]
 
Generated mesh with delta = 1.5 and volume-grading, [https://odu.box.com/s/tmmv1kjb925zclnshegypovxmaxablcs Output Mesh]
−
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Knee-Char.mha --delta 1.5 --volume-grading --output ./Knee-Char,d=1.5,grading.vtk</pre>
+
<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Knee-Char.mha --delta 1.5 --volume-grading --output ./Knee-Char,d=1.5,grading.vtk</pre>
  
 
[[File:Knee-Char,d=1.5,grading.png|500px|Knee-Char,d=1.5,grading.png]]
 
[[File:Knee-Char,d=1.5,grading.png|500px|Knee-Char,d=1.5,grading.png]]
Line 68: Line 68:
  
 
Generated mesh with delta = 5, [https://odu.box.com/s/ddja85vt80osbn76v7pih82wh0kiuqqp Output Mesh]
 
Generated mesh with delta = 5, [https://odu.box.com/s/ddja85vt80osbn76v7pih82wh0kiuqqp Output Mesh]
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<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Ircad2-Removed-Tissues.nrrd --delta 5 --output ./Ircad2-Removed-Tissues,d=5.vtk</pre>
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<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Ircad2-Removed-Tissues.nrrd --delta 5 --output ./Ircad2-Removed-Tissues,d=5.vtk</pre>
  
 
[[File:Ircad2-Removed-Tissues,d=5.png|500px|Ircad2-Removed-Tissues,d=5.png]]
 
[[File:Ircad2-Removed-Tissues,d=5.png|500px|Ircad2-Removed-Tissues,d=5.png]]

Revision as of 16:57, 26 February 2020

The directory containing the input data is Medical_Imaging_Data.

Head-Neck 2

  • Input distribution size : 1,000,000 cells
  • Uniform case: 768,033 tetrahedra
  • Adapted case: 264,762 tetrahedra
  • GPDMMS13 140519,d=1,uniform.png
  • GPDMMS13 140519,d=5,wl=0.05,me=1.png

Commands to generate meshes :

Uniform : Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./CNF_Data/3D/CFF_14052019/GPDMMS13_140519.nrrd --image-segmentation --linear-interpolation --output ./GPDMMS13_140519,d=1,uniform.vtk

Adapted : Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./CNF_Data/3D/CFF_14052019/GPDMMS13_140519.nrrd --cnf --weight-limit 0.05 --min-edge 1 --output ./GPDMMS13_140519,d=5,wl=0.05,me=1.vtk

Head-Neck

Input Image

Generated mesh with delta = 2, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Head-Neck.mha --delta 2 --output ./Head-Neck,d=2.vtk

Head-Neck,d=2.png

Generated mesh with delta = 1.5, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk

Head-Neck,d=1.5.png

Brain-With-Tumor-Case17

Input Image

Generated mesh with delta = 1,5, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Brain-With-Tumor-Case17.nii --delta 1.5 --output ./Brain-With-Tumor-Case17,d=1.5.vtk

Brain-With-Tumor-Case17,d=1.5.png

Generated mesh with delta = 1.5 and volume-grading, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Brain-With-Tumor-Case17.nii --delta 1.5 --volume-grading --output ./Brain-With-Tumor-Case17,d=1.5,grading.vtk

Brain-With-Tumor-Case17,d=1.5,grading.png

Knee-Char

Input Image

Generated mesh with delta = 1,5, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Knee-Char.mha --delta 1.5 --output ./Knee-Char,d=1.5.vtk

Knee-Char,d=1.5.png

Generated mesh with delta = 1.5 and volume-grading, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Knee-Char.mha --delta 1.5 --volume-grading --output ./Knee-Char,d=1.5,grading.vtk

Knee-Char,d=1.5,grading.png

Ircad2-Removed-Tissues

Input Image

Generated mesh with delta = 5, Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Ircad2-Removed-Tissues.nrrd --delta 5 --output ./Ircad2-Removed-Tissues,d=5.vtk

Ircad2-Removed-Tissues,d=5.png

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