Difference between revisions of "Medical Imaging Example Meshes"

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=Role of Delta=
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__TOC__
  
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The size of the input image is: (512x512x119)
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=3D Example Meshes=
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Spacing of the input image: (0.27734,0.27734,1)
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The directory containing the 3D input data is located in the 3D folder of [https://odu.box.com/s/olefferrnksu2nmerbfvbvsz2u4abbdw Medical_Imaging_Data].
  
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MinimumPhysicalSize = 119 * 1 = 119.
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==Ircad2==
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Max delta value that possibly will not cause problems is: 119 / 5 = 23.8
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* [https://odu.box.com/s/1ef11ry4yik5mny62dz6zyd9obqb540i Input Image]
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* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
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* Uniform with Delta = 2: 5,031,442 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
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* Graded with Delta = 1: 6,072,751 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
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* Uniform with Delta = 2 and excluded label 1: 1,941,468 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  
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==Table of produced number of Tetrahedra for certain values of delta using the image: Knee-Char.mha==
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<gallery mode="packed" heights=350px>
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{| class="wikitable"
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File:Ircad2,d=2.png
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! Delta !! # Vertices !! # Tetrahedra
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</gallery>
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|-
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<gallery mode="packed" heights=350px>
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| 23.8 || 70 || 153
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File:Ircad2,d=1,graded.png
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|-
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</gallery>
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| 20 || 87 || 222
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<gallery mode="packed" heights=350px>
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|-
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File:Ircad2,d=2,el=1.png
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| 15 || 219 || 668
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</gallery>
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|-
 
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| 10 || 551 || 1580
 
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|  5 || 2858 || 10073
 
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|  4 || 4544 || 16569
 
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|  3 || 9279 || 35131
 
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|-
 
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|  2 || 24631 || 98822
 
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|  1.5 || 50371 || 209659
 
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|  1 || 139515 || 613799
 
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|-
 
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|  0.5 || 830423 || 3999734
 
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|}
 
  
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=Head-Neck=
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Commands to generate meshes:
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[https://odu.box.com/s/09l553pqu319jdj3isam6dmukfy67ouq Input Image]
 
  
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Generated mesh with delta = 2, [https://odu.box.com/s/7kgv263qvebk55077nny4l2n7ienpahf Output Mesh]
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'''Uniform with Delta = 2:''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc 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>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 2 --threads 6 --output ./Ircad2,d=2.vtk
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</pre>
  
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[[File:Head-Neck,d=2.png|500px|Head-Neck,d=2.png]]
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'''Graded with Delta = 1:''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo Output Mesh]
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 1 --threads 6 --volume-grading --output ./Ircad2,d=1,graded.vtk
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</pre>
  
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Generated mesh with delta = 1.5, [https://odu.box.com/s/sfjb83whac8rhn1ykuuxmektprxtci78 Output Mesh]
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'''Uniform with Delta = 2 and excluded label 1:''' [https://odu.box.com/s/5jaukd6317jdmi8li479h8emknuw0rny Output Mesh]
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<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>
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --exclude-labels 1 --delta 2 --threads 6 --output ./Ircad2,d=2,el=1.vtk
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</pre>
  
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[[File:Head-Neck,d=1.5.png|500px|Head-Neck,d=1.5.png]]
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==Knee-Char==
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* [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf Input Image]
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* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
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* Uniform with Delta = default : 386,869 tetrahedra
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* Graded with Delta = default : 274,309 tetrahedra
  
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=Brain-With-Tumor-Case17=
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<gallery mode="packed" heights=350px>
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[https://odu.box.com/s/cjvg22e4txenhv1xh4mnqegowyfyut9y Input Image]
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File:Knee-Char,d=1.19.png
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</gallery>
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<gallery mode="packed" heights=350px>
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File:Knee-Char,d=1.19,graded.png
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</gallery>
  
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Generated mesh with delta = 1,5, [https://odu.box.com/s/wfeqw6c65si0kync8yi20cychyqxmpcs Output Mesh]
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Commands to generate meshes:
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<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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[[File:Brain-With-Tumor-Case17,d=1.5.png|500px|Brain-With-Tumor-Case17,d=1.5.png]]
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'''Uniform with Delta = default :''' [https://odu.box.com/s/q42ekuymr0gy0w882ilcngjfg8l95xvx Output Mesh]
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --output ./Knee-Char,d=1.19.vtk
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</pre>
  
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Generated mesh with delta = 1.5 and volume-grading, [https://odu.box.com/s/83pl6vgzabzclsbqyzujmtqjbfckil2s Output Mesh]
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'''Graded with Delta = default :''' [https://odu.box.com/s/i788xycxrd11wpxneo4wq3x0ekk9yemm Output Mesh]
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<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>
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --volume-grading --output ./Knee-Char,d=1.19,graded.vtk
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</pre>
  
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[[File:Brain-With-Tumor-Case17,d=1.5,grading.png|500px|Brain-With-Tumor-Case17,d=1.5,grading.png]]
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==Brain-With-Tumor-Case17==
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* [https://odu.box.com/s/ynudkxeozt5j82v1qmoovif10c73taw7 Input Image]
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* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
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* Uniform with Delta = default: 222,540 tetrahedra
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* Graded with Delta = default: 94,383 tetrahedra
  
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=Knee-Char=
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<gallery mode="packed" heights=350px>
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[https://odu.box.com/s/jr2a2nxb8uoidi78483fxk05ceplatmn Input Image]
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File:Brain-With-Tumor-Case17,d=1.76001.png
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</gallery>
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<gallery mode="packed" heights=350px>
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File:Brain-With-Tumor-Case17,d=1.76001,graded.png
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</gallery>
  
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Generated mesh with delta = 1,5, [https://odu.box.com/s/udhiz0u5bewtqi9z07owiejno9gjzb1j Output Mesh]
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Commands to generate meshes:
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<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>
 
  
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[[File:Knee-Char,d=1.5.png|500px|Knee-Char,d=1.5.png]]
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'''Uniform with Delta = default:''' [https://odu.box.com/s/5dqgw5pykve4xv2ii30xnkjq5s3maxdl Output Mesh]
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --output ./Brain-With-Tumor-Case17,d=1.76001.vtk
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</pre>
  
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Generated mesh with delta = 1.5 and volume-grading, [https://odu.box.com/s/tmmv1kjb925zclnshegypovxmaxablcs Output Mesh]
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'''Graded with Delta = default:''' [https://odu.box.com/s/8zlfyepfuzmd8g119eup5n2srxpbqg8s Output Mesh]
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<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>
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --volume-grading --output ./Brain-With-Tumor-Case17,d=1.76001,graded.vtk
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</pre>
  
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[[File:Knee-Char,d=1.5,grading.png|500px|Knee-Char,d=1.5,grading.png]]
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==Head-Neck==
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* [https://odu.box.com/s/zj492g475bo93kyrd1npmisy2gwdqorj Input Image]
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* Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
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* Uniform with Delta = default: 205,510 tetrahedra
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* Uniform with Delta = 1.5: 767,393 tetrahedra
  
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=Big-Brain=  
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<gallery mode="packed" heights=350px>
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[https://odu.box.com/s/jjsb3umvqf19xtzv3zlcmexuqfaq1frt Input Image]
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File:Head-Neck,d=2.49023.png
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</gallery>
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<gallery mode="packed" heights=350px>
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File:Head-Neck,d=1.5.png
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</gallery>
  
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Generated mesh with delta = 2, [https://odu.box.com/s/08v512e89woeiwdmrgi4wphh0f3njgt4 Output Mesh]
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Commands to generate meshes:
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<pre>docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./NRL_SHARE/Big-Brain.mha --delta 2 --output ./Big-Brain,d=2.vtk</pre>
 
  
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[[File:Big-Brain,d=2.png|500px|Big-Brain,d=2.png]]
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'''Uniform with Delta = default:''' [https://odu.box.com/s/zoi0em9twv0mgt2d1244yujtkd3nit3e Output Mesh]
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --output ./Head-Neck,d=2.49023.vtk
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</pre>
  
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=Ircad2-Removed-Tissues=
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'''Uniform with Delta = 1.5:''' [https://odu.box.com/s/jo4cwfrn1bvslocv9b11m0i9dhxyvdrc Output Mesh]
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[https://odu.box.com/s/01bxjptf4grfuvxj3a9g6frfosyu6dbt Input Image]
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<pre>
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docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk
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Generated mesh with delta = 5, [https://odu.box.com/s/ddja85vt80osbn76v7pih82wh0kiuqqp Output Mesh]
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</pre>
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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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[[File:Ircad2-Removed-Tissues,d=5.png|500px|Ircad2-Removed-Tissues,d=5.png]]
 

Latest revision as of 15:57, 2 June 2020

3D Example Meshes

The directory containing the 3D input data is located in the 3D folder of Medical_Imaging_Data.

Ircad2

  • Input Image
  • Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
  • Uniform with Delta = 2: 5,031,442 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  • Graded with Delta = 1: 6,072,751 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  • Uniform with Delta = 2 and excluded label 1: 1,941,468 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  • Ircad2,d=2.png
  • Ircad2,d=1,graded.png
  • Ircad2,d=2,el=1.png

Commands to generate meshes:

Uniform with Delta = 2: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 2 --threads 6 --output ./Ircad2,d=2.vtk

Graded with Delta = 1: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 1 --threads 6 --volume-grading --output ./Ircad2,d=1,graded.vtk

Uniform with Delta = 2 and excluded label 1: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --exclude-labels 1 --delta 2 --threads 6 --output ./Ircad2,d=2,el=1.vtk

Knee-Char

  • Input Image
  • Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
  • Uniform with Delta = default : 386,869 tetrahedra
  • Graded with Delta = default : 274,309 tetrahedra
  • Knee-Char,d=1.19.png
  • Knee-Char,d=1.19,graded.png

Commands to generate meshes:

Uniform with Delta = default : Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --output ./Knee-Char,d=1.19.vtk

Graded with Delta = default : Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --volume-grading --output ./Knee-Char,d=1.19,graded.vtk

Brain-With-Tumor-Case17

  • Input Image
  • Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
  • Uniform with Delta = default: 222,540 tetrahedra
  • Graded with Delta = default: 94,383 tetrahedra
  • Brain-With-Tumor-Case17,d=1.76001.png
  • Brain-With-Tumor-Case17,d=1.76001,graded.png

Commands to generate meshes:

Uniform with Delta = default: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --output ./Brain-With-Tumor-Case17,d=1.76001.vtk

Graded with Delta = default: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --volume-grading --output ./Brain-With-Tumor-Case17,d=1.76001,graded.vtk

Head-Neck

  • Input Image
  • Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
  • Uniform with Delta = default: 205,510 tetrahedra
  • Uniform with Delta = 1.5: 767,393 tetrahedra
  • Head-Neck,d=2.49023.png
  • Head-Neck,d=1.5.png

Commands to generate meshes:

Uniform with Delta = default: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --output ./Head-Neck,d=2.49023.vtk

Uniform with Delta = 1.5: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk
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